rs4680612

Positions:

• chr3-165891643-G-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;