rs4648942

Variant names:

• chr1-24150967-T-C
• rs4648942

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 0.547 in 152,026 control chromosomes in the GnomAD database, including 23,058 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 0.55 (23058 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.402
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.565 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.547 AC: 83134 AN: 151908 Hom.: 23040 Cov.: 32

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.679

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.547 AC: 83198 AN: 152026 Hom.: 23058 Cov.: 32 AF XY: 0.549 AC XY: 40821 AN XY: 74300

African (AFR) AF: 0.519 AC: 21538 AN: 41466

American (AMR) AF: 0.575 AC: 8792 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.554 AC: 1923 AN: 3470

East Asian (EAS) AF: 0.313 AC: 1615 AN: 5166

South Asian (SAS) AF: 0.456 AC: 2193 AN: 4808

European-Finnish (FIN) AF: 0.679 AC: 7174 AN: 10560

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.561 AC: 38118 AN: 67962

Other (OTH) AF: 0.575 AC: 1212 AN: 2106

Alfa AF: 0.561 Hom.: 2982

Bravo AF: 0.539

Asia WGS AF: 0.410 AC: 1422 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.58
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs4648942; hg19: chr1-24477457;