rs4657958

Variant names:

• chr1-195084699-G-A
• rs4657958

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 0.341 in 151,770 control chromosomes in the GnomAD database, including 9,149 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 0.34 (9149 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.158
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.4 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: 0.341 AC: 51708 AN: 151652 Hom.: 9126 Cov.: 32

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.324

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.414

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.385

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.341 AC: 51776 AN: 151770 Hom.: 9149 Cov.: 32 AF XY: 0.337 AC XY: 25005 AN XY: 74170

African (AFR) AF: 0.399 AC: 16531 AN: 41392

American (AMR) AF: 0.309 AC: 4711 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.433 AC: 1498 AN: 3462

East Asian (EAS) AF: 0.414 AC: 2126 AN: 5130

South Asian (SAS) AF: 0.336 AC: 1622 AN: 4828

European-Finnish (FIN) AF: 0.232 AC: 2453 AN: 10560

Middle Eastern (MID) AF: 0.384 AC: 112 AN: 292

European-Non Finnish (NFE) AF: 0.319 AC: 21666 AN: 67858

Other (OTH) AF: 0.361 AC: 762 AN: 2110

Alfa AF: 0.319 Hom.: 1349

Bravo AF: 0.348

Asia WGS AF: 0.429 AC: 1492 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.25
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs4657958; hg19: chr1-195053829;