rs4655567

Positions:

• chr1-67635957-G-C
• chr1-67635957-G-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 0.165 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.374

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.0121

Gnomad4 EAS AF: 0.313

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.0528

Gnomad4 OTH AF: 0.142

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4655567; hg19: chr1-68101640;