rs79389707

Variant names:

• chr20-62353047-C-T
• rs79389707
• NM_005560.6:c.568+87G>A

Your query was ambiguous. Multiple possible variants found:

• chr20-62353047-C-T
• chr20-62353047-C-G

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_005560.6(LAMA5):​c.568+87G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00609 in 954,802 control chromosomes in the GnomAD database, including 219 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.024 (137 hom., cov: 33)
  • Exomes 𝑓: 0.0027 (82 hom.)
• Consequence: LAMA5 NM_005560.6 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.397
• Publications: 0 publications found

Genes affected

LAMA5 (HGNC:6485): (laminin subunit alpha 5) This gene encodes one of the vertebrate laminin alpha chains. Laminins, a family of extracellular matrix glycoproteins, are the major noncollagenous constituent of basement membranes. They have been implicated in a wide variety of biological processes including cell adhesion, differentiation, migration, signaling, neurite outgrowth and metastasis. Laminins are composed of 3 non identical chains: laminin alpha, beta and gamma (formerly A, B1, and B2, respectively) and they form a cruciform structure consisting of 3 short arms, each formed by a different chain, and a long arm composed of all 3 chains. Each laminin chain is a multidomain protein encoded by a distinct gene. The protein encoded by this gene is the alpha-5 subunit of of laminin-10 (laminin-511), laminin-11 (laminin-521) and laminin-15 (laminin-523). [provided by RefSeq, Jun 2013]

LAMA5-AS1 (HGNC:40334): (LAMA5 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BP6: Variant 20-62353047-C-T is Benign according to our data. Variant chr20-62353047-C-T is described in ClinVar as Benign. ClinVar VariationId is 1259215.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0805 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005560.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LAMA5	NM_005560.6	MANE Select	c.568+87G>A		intron	N/A	NP_005551.3
	LAMA5-AS1	NR_109922.1		n.38C>T		non_coding_transcript_exon	Exon 1 of 3
	LAMA5-AS1	NR_109923.1		n.38C>T		non_coding_transcript_exon	Exon 1 of 2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LAMA5	ENST00000252999.7	TSL:1 MANE Select	c.568+87G>A		intron	N/A	ENSP00000252999.3	O15230-1
	LAMA5-AS1	ENST00000456721.5	TSL:2	n.78C>T		non_coding_transcript_exon	Exon 1 of 2
	LAMA5-AS1	ENST00000477848.5	TSL:3	n.38C>T		non_coding_transcript_exon	Exon 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0238 AC: 3617 AN: 152118 Hom.: 135 Cov.: 33

Gnomad AFR AF: 0.0827

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00805

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00394

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.000279

Gnomad OTH AF: 0.0139

GnomAD4 exome AF: 0.00273 AC: 2191 AN: 802566 Hom.: 82 Cov.: 11 AF XY: 0.00260 AC XY: 1065 AN XY: 409994

African (AFR) AF: 0.0819 AC: 1552 AN: 18940

American (AMR) AF: 0.00421 AC: 107 AN: 25390

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 17340

East Asian (EAS) AF: 0.0000622 AC: 2 AN: 32150

South Asian (SAS) AF: 0.00431 AC: 250 AN: 57962

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 43912

Middle Eastern (MID) AF: 0.00327 AC: 11 AN: 3366

European-Non Finnish (NFE) AF: 0.000140 AC: 79 AN: 565798

Other (OTH) AF: 0.00504 AC: 190 AN: 37708

GnomAD4 genome AF: 0.0238 AC: 3628 AN: 152236 Hom.: 137 Cov.: 33 AF XY: 0.0229 AC XY: 1707 AN XY: 74432

African (AFR) AF: 0.0828 AC: 3437 AN: 41526

American (AMR) AF: 0.00804 AC: 123 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5172

South Asian (SAS) AF: 0.00394 AC: 19 AN: 4818

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10624

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.000279 AC: 19 AN: 68006

Other (OTH) AF: 0.0137 AC: 29 AN: 2114

Alfa AF: 0.0207 Hom.: 20

Bravo AF: 0.0259

Asia WGS AF: 0.00924 AC: 32 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.85
DANN	Benign	0.76
PhyloP100		-0.40
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs79389707; hg19: chr20-60928103;