rs4655567

Variant names:

• chr1-67635957-G-C
• rs4655567

Your query was ambiguous. Multiple possible variants found:

• chr1-67635957-G-C
• chr1-67635957-G-T

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 0.165 in 151,986 control chromosomes in the GnomAD database, including 3,622 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 0.17 (3622 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• 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 (AFR) allele frequency at 95% confidence interval = 0.369 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: 0.165 AC: 25017 AN: 151868 Hom.: 3603 Cov.: 32

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.0121

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0528

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.165 AC: 25078 AN: 151986 Hom.: 3622 Cov.: 32 AF XY: 0.169 AC XY: 12582 AN XY: 74290

African (AFR) AF: 0.374 AC: 15474 AN: 41392

American (AMR) AF: 0.124 AC: 1901 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0121 AC: 42 AN: 3468

East Asian (EAS) AF: 0.313 AC: 1614 AN: 5160

South Asian (SAS) AF: 0.183 AC: 883 AN: 4814

European-Finnish (FIN) AF: 0.116 AC: 1227 AN: 10550

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0528 AC: 3594 AN: 68012

Other (OTH) AF: 0.142 AC: 300 AN: 2106

Alfa AF: 0.118 Hom.: 247

Bravo AF: 0.172

Asia WGS AF: 0.261 AC: 907 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	0.12
DANN	Benign	0.61
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs4655567; hg19: chr1-68101640;