rs560994

Positions:

• chr3-172436230-T-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 0.621 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.680

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.172436230T>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;