6-112280719-C-T

Position:

• chr6-112280719-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_121193.1(LAMA4-AS1):​n.182-25610C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 152,064 control chromosomes in the GnomAD database, including 2,972 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 0.17 (2972 hom., cov: 32)
• Consequence: LAMA4-AS1 NR_121193.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00400

Genes affected

LAMA4-AS1 (HGNC:40333): (LAMA4 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LAMA4-AS1	NR_121193.1	n.182-25610C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LAMA4-AS1	ENST00000433684.6	n.685-25610C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.171 AC: 25923 AN: 151946 Hom.: 2968 Cov.: 32

Gnomad AFR AF: 0.0674

Gnomad AMI AF: 0.0943

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.0928

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.171 AC: 25936 AN: 152064 Hom.: 2972 Cov.: 32 AF XY: 0.178 AC XY: 13250 AN XY: 74324

Gnomad4 AFR AF: 0.0673

Gnomad4 AMR AF: 0.322

Gnomad4 ASJ AF: 0.0928

Gnomad4 EAS AF: 0.486

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.240

Gnomad4 NFE AF: 0.165

Gnomad4 OTH AF: 0.167

Alfa AF: 0.158 Hom.: 4077

Bravo AF: 0.176

Asia WGS AF: 0.348 AC: 1210 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.6
DANN	Benign	0.43

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

Publications

LitVar

Other links and lift over

dbSNP: rs17073644; hg19: chr6-112601921; COSMIC: COSV70931959; COSMIC: COSV70931959;