rs6687813

Variant names:

• chr1-169508336-A-C
• rs6687813

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 0.927 in 152,184 control chromosomes in the GnomAD database, including 65,391 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 0.93 (65391 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.513
• Publications: 26 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.927 AC: 140905 AN: 152066 Hom.: 65334 Cov.: 32

Gnomad AFR AF: 0.896

Gnomad AMI AF: 0.893

Gnomad AMR AF: 0.950

Gnomad ASJ AF: 0.875

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.933

Gnomad FIN AF: 0.951

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.934

Gnomad OTH AF: 0.924

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

GnomAD4 genome AF: 0.927 AC: 141021 AN: 152184 Hom.: 65391 Cov.: 32 AF XY: 0.928 AC XY: 69072 AN XY: 74402

African (AFR) AF: 0.896 AC: 37180 AN: 41496

American (AMR) AF: 0.951 AC: 14511 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.875 AC: 3037 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5184 AN: 5186

South Asian (SAS) AF: 0.934 AC: 4508 AN: 4828

European-Finnish (FIN) AF: 0.951 AC: 10090 AN: 10612

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.934 AC: 63493 AN: 68008

Other (OTH) AF: 0.925 AC: 1954 AN: 2112

Alfa AF: 0.929 Hom.: 184945

Bravo AF: 0.925

Asia WGS AF: 0.973 AC: 3385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.76
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs6687813; hg19: chr1-169477574;