rs1722791

Variant names:

• chr15-23707591-A-C
• rs1722791

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 0.473 in 152,022 control chromosomes in the GnomAD database, including 17,321 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 0.47 (17321 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.744

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.532 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: 0.473 AC: 71806 AN: 151902 Hom.: 17307 Cov.: 32

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.452

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.473 AC: 71853 AN: 152022 Hom.: 17321 Cov.: 32 AF XY: 0.467 AC XY: 34718 AN XY: 74296

Gnomad4 AFR AF: 0.390

Gnomad4 AMR AF: 0.458

Gnomad4 ASJ AF: 0.449

Gnomad4 EAS AF: 0.363

Gnomad4 SAS AF: 0.428

Gnomad4 FIN AF: 0.496

Gnomad4 NFE AF: 0.536

Gnomad4 OTH AF: 0.469

Alfa AF: 0.516 Hom.: 42647

Bravo AF: 0.467

Asia WGS AF: 0.384 AC: 1331 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.5
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1722791; hg19: chr15-23952738;