rs1953273

Variant names:

• chr14-31899728-A-G
• rs1953273

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.61 in 151,208 control chromosomes in the GnomAD database, including 28,911 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 0.61 (28911 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.689
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.757 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: 0.610 AC: 92106 AN: 151090 Hom.: 28884 Cov.: 29

Gnomad AFR AF: 0.764

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.553

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.610 AC: 92180 AN: 151208 Hom.: 28911 Cov.: 29 AF XY: 0.611 AC XY: 45081 AN XY: 73814

African (AFR) AF: 0.764 AC: 31393 AN: 41096

American (AMR) AF: 0.533 AC: 8095 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.488 AC: 1695 AN: 3470

East Asian (EAS) AF: 0.475 AC: 2446 AN: 5152

South Asian (SAS) AF: 0.621 AC: 2969 AN: 4778

European-Finnish (FIN) AF: 0.596 AC: 6147 AN: 10310

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.553 AC: 37565 AN: 67898

Other (OTH) AF: 0.583 AC: 1225 AN: 2102

Alfa AF: 0.559 Hom.: 92447

Bravo AF: 0.608

Asia WGS AF: 0.527 AC: 1837 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.74
DANN	Benign	0.54
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs1953273; hg19: chr14-32368934;