rs324702

Positions:

• chr4-75816637-C-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.726

Gnomad4 AMR AF: 0.850

Gnomad4 ASJ AF: 0.851

Gnomad4 EAS AF: 0.994

Gnomad4 SAS AF: 0.873

Gnomad4 FIN AF: 0.815

Gnomad4 NFE AF: 0.795

Gnomad4 OTH AF: 0.813

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs324702; hg19: chr4-76737790;