rs7676384

chr4-161252328-C-T

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 0.193 in 150,234 control chromosomes in the GnomAD database, including 2,890 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 0.19 (2890 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.662

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.193 AC: 28968 AN: 150116 Hom.: 2883 Cov.: 31

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.193 AC: 29002 AN: 150234 Hom.: 2890 Cov.: 31 AF XY: 0.193 AC XY: 14183 AN XY: 73474

Gnomad4 AFR AF: 0.227

Gnomad4 AMR AF: 0.208

Gnomad4 ASJ AF: 0.166

Gnomad4 EAS AF: 0.283

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.177

Gnomad4 OTH AF: 0.191

Alfa AF: 0.180 Hom.: 306

Bravo AF: 0.194

Asia WGS AF: 0.190 AC: 659 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	6.6
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7676384; hg19: chr4-162173480;