rs647008

Variant names:

• chr1-67679256-A-G
• rs647008

Your query was ambiguous. Multiple possible variants found:

• chr1-67679256-A-G
• chr1-67679256-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 0.196 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.294

Gnomad4 AMR AF: 0.172

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.127

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.181

Alfa AF: 0.126 Hom.: 435

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs647008; hg19: chr1-68144939;