rs560994

Variant names:

• chr3-172436230-T-A
• rs560994

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 0.621 in 151,888 control chromosomes in the GnomAD database, including 30,489 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 0.62 (30489 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.680

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.713 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: 0.621 AC: 94296 AN: 151770 Hom.: 30486 Cov.: 31

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.725

Gnomad AMR AF: 0.688

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.718

Gnomad OTH AF: 0.653

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

GnomAD4 genome AF: 0.621 AC: 94327 AN: 151888 Hom.: 30489 Cov.: 31 AF XY: 0.618 AC XY: 45881 AN XY: 74206

Gnomad4 AFR AF: 0.431

Gnomad4 AMR AF: 0.688

Gnomad4 ASJ AF: 0.659

Gnomad4 EAS AF: 0.630

Gnomad4 SAS AF: 0.457

Gnomad4 FIN AF: 0.688

Gnomad4 NFE AF: 0.718

Gnomad4 OTH AF: 0.654

Alfa AF: 0.661 Hom.: 4242

Bravo AF: 0.620

Asia WGS AF: 0.522 AC: 1820 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.60
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs560994; hg19: chr3-172154020;