rs4680612

Variant names:

• chr3-165891643-G-A
• rs4680612

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 0.946 in 152,280 control chromosomes in the GnomAD database, including 68,140 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 0.95 (68140 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66

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 (NFE) allele frequency at 95% confidence interval = 0.957 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: 0.946 AC: 143881 AN: 152162 Hom.: 68091 Cov.: 32

Gnomad AFR AF: 0.905

Gnomad AMI AF: 0.984

Gnomad AMR AF: 0.961

Gnomad ASJ AF: 0.970

Gnomad EAS AF: 0.915

Gnomad SAS AF: 0.919

Gnomad FIN AF: 0.985

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.963

Gnomad OTH AF: 0.946

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

GnomAD4 genome AF: 0.946 AC: 143991 AN: 152280 Hom.: 68140 Cov.: 32 AF XY: 0.947 AC XY: 70472 AN XY: 74452

Gnomad4 AFR AF: 0.905

Gnomad4 AMR AF: 0.961

Gnomad4 ASJ AF: 0.970

Gnomad4 EAS AF: 0.915

Gnomad4 SAS AF: 0.919

Gnomad4 FIN AF: 0.985

Gnomad4 NFE AF: 0.963

Gnomad4 OTH AF: 0.947

Alfa AF: 0.960 Hom.: 16380

Bravo AF: 0.941

Asia WGS AF: 0.933 AC: 3245 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	0.088
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4680612; hg19: chr3-165609431;