rs324702

Variant names:

• chr4-75816637-C-G
• rs324702

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 0.794 in 152,156 control chromosomes in the GnomAD database, including 48,231 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 0.79 (48231 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.566
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 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: 0.794 AC: 120686 AN: 152038 Hom.: 48183 Cov.: 32

Gnomad AFR AF: 0.726

Gnomad AMI AF: 0.771

Gnomad AMR AF: 0.850

Gnomad ASJ AF: 0.851

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.872

Gnomad FIN AF: 0.815

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.812

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

GnomAD4 genome AF: 0.794 AC: 120792 AN: 152156 Hom.: 48231 Cov.: 32 AF XY: 0.798 AC XY: 59393 AN XY: 74404

African (AFR) AF: 0.726 AC: 30114 AN: 41470

American (AMR) AF: 0.850 AC: 13012 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.851 AC: 2954 AN: 3472

East Asian (EAS) AF: 0.994 AC: 5150 AN: 5182

South Asian (SAS) AF: 0.873 AC: 4204 AN: 4818

European-Finnish (FIN) AF: 0.815 AC: 8635 AN: 10590

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.795 AC: 54050 AN: 68006

Other (OTH) AF: 0.813 AC: 1717 AN: 2112

Alfa AF: 0.792 Hom.: 5974

Bravo AF: 0.792

Asia WGS AF: 0.906 AC: 3148 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.86
DANN	Benign	0.59
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs324702; hg19: chr4-76737790;