rs4657270

Variant names:

• chr1-163408857-G-A
• rs4657270

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 0.0437 in 152,218 control chromosomes in the GnomAD database, including 198 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 0.044 (198 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.462
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0601 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0438 AC: 6661 AN: 152100 Hom.: 198 Cov.: 33

Gnomad AFR AF: 0.00997

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0407

Gnomad ASJ AF: 0.0476

Gnomad EAS AF: 0.0333

Gnomad SAS AF: 0.0294

Gnomad FIN AF: 0.0798

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0617

Gnomad OTH AF: 0.0349

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

GnomAD4 genome AF: 0.0437 AC: 6659 AN: 152218 Hom.: 198 Cov.: 33 AF XY: 0.0434 AC XY: 3232 AN XY: 74422

African (AFR) AF: 0.00994 AC: 413 AN: 41564

American (AMR) AF: 0.0406 AC: 621 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0476 AC: 165 AN: 3470

East Asian (EAS) AF: 0.0334 AC: 173 AN: 5178

South Asian (SAS) AF: 0.0293 AC: 141 AN: 4820

European-Finnish (FIN) AF: 0.0798 AC: 845 AN: 10588

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0617 AC: 4192 AN: 67990

Other (OTH) AF: 0.0345 AC: 73 AN: 2114

Alfa AF: 0.0547 Hom.: 412

Bravo AF: 0.0402

Asia WGS AF: 0.0330 AC: 115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.24
DANN	Benign	0.43
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs4657270; hg19: chr1-163378647;