rs1716543

Variant names:

• chr12-80936161-A-C
• rs1716543
• NM_004664.4:c.82+1480T>G

Your query was ambiguous. Multiple possible variants found:

• chr12-80936161-A-C
• chr12-80936161-A-T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_004664.4(LIN7A):​c.82+1480T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.638 in 152,040 control chromosomes in the GnomAD database, including 34,081 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.64 (34081 hom., cov: 32)
• Consequence: LIN7A NM_004664.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.65
• Publications: 5 publications found

Genes affected

LIN7A (HGNC:17787): (lin-7 homolog A, crumbs cell polarity complex component) The protein encoded by this gene is involved in generating and maintaining the asymmetric distribution of channels and receptors at the cell membrane. The encoded protein also is required for the localization of some specific channels and can be part of a protein complex that couples synaptic vesicle exocytosis to cell adhesion in the brain. [provided by RefSeq, May 2016]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.797 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004664.4. 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
	LIN7A	NM_004664.4	MANE Select	c.82+1480T>G		intron	N/A	NP_004655.1	O14910
	LIN7A	NM_001324423.2		c.-13+1480T>G		intron	N/A	NP_001311352.1
	LIN7A	NR_136887.2		n.67+1480T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LIN7A	ENST00000552864.6	TSL:1 MANE Select	c.82+1480T>G		intron	N/A	ENSP00000447488.1	O14910
	LIN7A	ENST00000549417.5	TSL:1	c.64+1480T>G		intron	N/A	ENSP00000448975.1	H0YIA8
	LIN7A	ENST00000261203.7	TSL:1	n.82+1480T>G		intron	N/A	ENSP00000261203.3	J3KN23

Frequencies

GnomAD3 genomes AF: 0.638 AC: 96979 AN: 151922 Hom.: 34090 Cov.: 32

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.799

Gnomad AMR AF: 0.673

Gnomad ASJ AF: 0.722

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.751

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.803

Gnomad OTH AF: 0.692

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.638 AC: 97004 AN: 152040 Hom.: 34081 Cov.: 32 AF XY: 0.635 AC XY: 47233 AN XY: 74328

African (AFR) AF: 0.327 AC: 13558 AN: 41466

American (AMR) AF: 0.673 AC: 10280 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.722 AC: 2505 AN: 3470

East Asian (EAS) AF: 0.552 AC: 2848 AN: 5164

South Asian (SAS) AF: 0.605 AC: 2905 AN: 4804

European-Finnish (FIN) AF: 0.751 AC: 7938 AN: 10576

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.803 AC: 54560 AN: 67968

Other (OTH) AF: 0.689 AC: 1449 AN: 2104

Alfa AF: 0.760 Hom.: 74965

Bravo AF: 0.622

Asia WGS AF: 0.564 AC: 1961 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	15
DANN	Benign	0.79
PhyloP100		2.6
Mutation Taster		=100/0	polymorphism (auto)

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: rs1716543; hg19: chr12-81329940;