rs4308924

Variant names:

• chr1-232691597-T-C
• rs4308924

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 0.136 in 152,140 control chromosomes in the GnomAD database, including 2,117 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 0.14 (2117 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.285 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: 0.136 AC: 20618 AN: 152022 Hom.: 2102 Cov.: 31

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.0710

Gnomad ASJ AF: 0.0666

Gnomad EAS AF: 0.0687

Gnomad SAS AF: 0.0920

Gnomad FIN AF: 0.0913

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0764

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.136 AC: 20678 AN: 152140 Hom.: 2117 Cov.: 31 AF XY: 0.133 AC XY: 9895 AN XY: 74376

African (AFR) AF: 0.290 AC: 12011 AN: 41444

American (AMR) AF: 0.0709 AC: 1084 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0666 AC: 231 AN: 3470

East Asian (EAS) AF: 0.0683 AC: 353 AN: 5168

South Asian (SAS) AF: 0.0916 AC: 441 AN: 4812

European-Finnish (FIN) AF: 0.0913 AC: 969 AN: 10614

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0765 AC: 5201 AN: 68016

Other (OTH) AF: 0.124 AC: 261 AN: 2112

Alfa AF: 0.101 Hom.: 329

Bravo AF: 0.140

Asia WGS AF: 0.106 AC: 368 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.27
DANN	Benign	0.68
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs4308924; hg19: chr1-232827343;