rs2981464

Positions:

• chr3-172450502-A-G
• chr3-172450502-A-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 0.553 in 151,992 control chromosomes in the GnomAD database, including 23,620 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 0.55 (23620 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.652 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: 0.553 AC: 83923 AN: 151874 Hom.: 23596 Cov.: 32

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.520

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.509

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.553 AC: 83992 AN: 151992 Hom.: 23620 Cov.: 32 AF XY: 0.551 AC XY: 40927 AN XY: 74272

Gnomad4 AFR AF: 0.659

Gnomad4 AMR AF: 0.521

Gnomad4 ASJ AF: 0.561

Gnomad4 EAS AF: 0.389

Gnomad4 SAS AF: 0.592

Gnomad4 FIN AF: 0.522

Gnomad4 NFE AF: 0.509

Gnomad4 OTH AF: 0.562

Alfa AF: 0.539 Hom.: 2768

Bravo AF: 0.556

Asia WGS AF: 0.544 AC: 1888 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.65
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2981464; hg19: chr3-172168292;