1-67679256-A-G

Variant names:

• chr1-67679256-A-G
• rs647008

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 0.196 in 152,136 control chromosomes in the GnomAD database, including 3,258 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 0.20 (3258 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.29 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: 0.196 AC: 29841 AN: 152018 Hom.: 3258 Cov.: 31

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.196 AC: 29878 AN: 152136 Hom.: 3258 Cov.: 31 AF XY: 0.197 AC XY: 14654 AN XY: 74388

African (AFR) AF: 0.294 AC: 12203 AN: 41484

American (AMR) AF: 0.172 AC: 2633 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 515 AN: 3452

East Asian (EAS) AF: 0.127 AC: 657 AN: 5192

South Asian (SAS) AF: 0.157 AC: 759 AN: 4832

European-Finnish (FIN) AF: 0.197 AC: 2081 AN: 10574

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10511 AN: 68010

Other (OTH) AF: 0.181 AC: 381 AN: 2106

Alfa AF: 0.132 Hom.: 540

Bravo AF: 0.197

Asia WGS AF: 0.173 AC: 601 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.10
DANN	Benign	0.50
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs647008; hg19: chr1-68144939;