chr15-101158771-A-G

Variant names:

• chr15-101158771-A-G
• rs11247268

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 0.33 in 152,050 control chromosomes in the GnomAD database, including 9,277 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 0.33 (9277 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.102
• Publications: 6 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 (EAS) allele frequency at 95% confidence interval = 0.835 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: 0.330 AC: 50102 AN: 151932 Hom.: 9276 Cov.: 32

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.856

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.330 AC: 50133 AN: 152050 Hom.: 9277 Cov.: 32 AF XY: 0.338 AC XY: 25125 AN XY: 74324

African (AFR) AF: 0.245 AC: 10155 AN: 41480

American (AMR) AF: 0.355 AC: 5422 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 1114 AN: 3470

East Asian (EAS) AF: 0.856 AC: 4425 AN: 5172

South Asian (SAS) AF: 0.508 AC: 2448 AN: 4818

European-Finnish (FIN) AF: 0.356 AC: 3756 AN: 10564

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.320 AC: 21714 AN: 67954

Other (OTH) AF: 0.325 AC: 687 AN: 2114

Alfa AF: 0.334 Hom.: 7480

Bravo AF: 0.324

Asia WGS AF: 0.654 AC: 2274 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.49
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs11247268; hg19: chr15-101698976;