chr15-23707591-A-C

Variant names:

• chr15-23707591-A-C
• rs1722791

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 0.473 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
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• 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

African (AFR) AF: 0.390 AC: 16194 AN: 41488

American (AMR) AF: 0.458 AC: 6990 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.449 AC: 1560 AN: 3472

East Asian (EAS) AF: 0.363 AC: 1866 AN: 5146

South Asian (SAS) AF: 0.428 AC: 2066 AN: 4822

European-Finnish (FIN) AF: 0.496 AC: 5216 AN: 10522

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.536 AC: 36445 AN: 67978

Other (OTH) AF: 0.469 AC: 990 AN: 2112

Alfa AF: 0.510 Hom.: 63060

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
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs1722791; hg19: chr15-23952738;