rs6662567

Variant names:

• chr1-164547612-C-T
• rs6662567

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 0.218 in 152,042 control chromosomes in the GnomAD database, including 4,981 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 0.22 (4981 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.721
• Publications: 5 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 = 0.619 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: 0.219 AC: 33203 AN: 151924 Hom.: 4974 Cov.: 32

Gnomad AFR AF: 0.0478

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.636

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.218 AC: 33220 AN: 152042 Hom.: 4981 Cov.: 32 AF XY: 0.227 AC XY: 16856 AN XY: 74310

African (AFR) AF: 0.0477 AC: 1981 AN: 41508

American (AMR) AF: 0.348 AC: 5316 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 688 AN: 3470

East Asian (EAS) AF: 0.637 AC: 3278 AN: 5146

South Asian (SAS) AF: 0.394 AC: 1898 AN: 4820

European-Finnish (FIN) AF: 0.240 AC: 2533 AN: 10568

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.246 AC: 16744 AN: 67964

Other (OTH) AF: 0.221 AC: 466 AN: 2106

Alfa AF: 0.229 Hom.: 612

Bravo AF: 0.221

Asia WGS AF: 0.457 AC: 1587 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	0.47
DANN	Benign	0.54
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs6662567; hg19: chr1-164516849;