rs6811401

Variant names:

• chr4-38163669-T-G
• rs6811401

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0857 in 152,160 control chromosomes in the GnomAD database, including 1,392 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 0.086 (1392 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.709
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.248 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0854 AC: 12990 AN: 152042 Hom.: 1378 Cov.: 32

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0453

Gnomad ASJ AF: 0.0211

Gnomad EAS AF: 0.0541

Gnomad SAS AF: 0.0778

Gnomad FIN AF: 0.0175

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0122

Gnomad OTH AF: 0.0680

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

GnomAD4 genome AF: 0.0857 AC: 13044 AN: 152160 Hom.: 1392 Cov.: 32 AF XY: 0.0850 AC XY: 6321 AN XY: 74388

African (AFR) AF: 0.252 AC: 10457 AN: 41430

American (AMR) AF: 0.0452 AC: 692 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0211 AC: 73 AN: 3466

East Asian (EAS) AF: 0.0542 AC: 281 AN: 5186

South Asian (SAS) AF: 0.0776 AC: 375 AN: 4830

European-Finnish (FIN) AF: 0.0175 AC: 186 AN: 10618

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0122 AC: 829 AN: 68010

Other (OTH) AF: 0.0682 AC: 144 AN: 2110

Alfa AF: 0.0278 Hom.: 217

Bravo AF: 0.0932

Asia WGS AF: 0.0860 AC: 299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	15
DANN	Benign	0.79
PhyloP100		0.71

Splicing

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

Other links and lift over

dbSNP: rs6811401; hg19: chr4-38165290;