rs3812163

Positions:

• chr6-7725527-A-T

Variant summary

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

The variant allele was found at a frequency of 0.385 in 151,886 control chromosomes in the GnomAD database, including 11,826 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 0.39 (11826 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.385 AC: 58498 AN: 151768 Hom.: 11825 Cov.: 31

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.385 AC: 58525 AN: 151886 Hom.: 11826 Cov.: 31 AF XY: 0.381 AC XY: 28315 AN XY: 74236

Gnomad4 AFR AF: 0.281

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.238

Gnomad4 SAS AF: 0.529

Gnomad4 FIN AF: 0.440

Gnomad4 NFE AF: 0.457

Gnomad4 OTH AF: 0.360

Alfa AF: 0.424 Hom.: 1695

Bravo AF: 0.366

Asia WGS AF: 0.344 AC: 1198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.5
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3812163; hg19: chr6-7725760;