chr4-102076176-T-C

Variant names:

• chr4-102076176-T-C
• rs7692330

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 0.918 in 152,180 control chromosomes in the GnomAD database, including 64,298 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 0.92 (64298 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.500

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.926 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: 0.919 AC: 139696 AN: 152062 Hom.: 64266 Cov.: 31

Gnomad AFR AF: 0.923

Gnomad AMI AF: 0.946

Gnomad AMR AF: 0.912

Gnomad ASJ AF: 0.949

Gnomad EAS AF: 0.844

Gnomad SAS AF: 0.818

Gnomad FIN AF: 0.894

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.932

Gnomad OTH AF: 0.924

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

GnomAD4 genome AF: 0.918 AC: 139774 AN: 152180 Hom.: 64298 Cov.: 31 AF XY: 0.915 AC XY: 68040 AN XY: 74386

Gnomad4 AFR AF: 0.923

Gnomad4 AMR AF: 0.910

Gnomad4 ASJ AF: 0.949

Gnomad4 EAS AF: 0.844

Gnomad4 SAS AF: 0.818

Gnomad4 FIN AF: 0.894

Gnomad4 NFE AF: 0.932

Gnomad4 OTH AF: 0.921

Alfa AF: 0.932 Hom.: 6357

Bravo AF: 0.924

Asia WGS AF: 0.843 AC: 2935 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.1
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7692330; hg19: chr4-102997333;