15-69157508-T-C

Variant names:

• chr15-69157508-T-C
• rs1553251

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 0.705 in 152,150 control chromosomes in the GnomAD database, including 37,941 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 0.71 (37941 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.40
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.744 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: 0.705 AC: 107196 AN: 152032 Hom.: 37900 Cov.: 33

Gnomad AFR AF: 0.685

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.755

Gnomad ASJ AF: 0.670

Gnomad EAS AF: 0.726

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.705

Gnomad MID AF: 0.637

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.710

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

GnomAD4 genome AF: 0.705 AC: 107283 AN: 152150 Hom.: 37941 Cov.: 33 AF XY: 0.705 AC XY: 52418 AN XY: 74384

African (AFR) AF: 0.685 AC: 28427 AN: 41482

American (AMR) AF: 0.755 AC: 11552 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.670 AC: 2324 AN: 3470

East Asian (EAS) AF: 0.725 AC: 3753 AN: 5176

South Asian (SAS) AF: 0.593 AC: 2865 AN: 4828

European-Finnish (FIN) AF: 0.705 AC: 7465 AN: 10582

Middle Eastern (MID) AF: 0.640 AC: 187 AN: 292

European-Non Finnish (NFE) AF: 0.714 AC: 48568 AN: 67998

Other (OTH) AF: 0.705 AC: 1491 AN: 2116

Alfa AF: 0.695 Hom.: 16419

Bravo AF: 0.713

Asia WGS AF: 0.645 AC: 2242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	7.8
DANN	Benign	0.32
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs1553251; hg19: chr15-69449847;