rs11073742

Variant names:

• chr15-87816062-T-A
• rs11073742

Your query was ambiguous. Multiple possible variants found:

• chr15-87816062-T-A
• chr15-87816062-T-G

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 0.349 in 151,890 control chromosomes in the GnomAD database, including 9,599 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 0.35 (9599 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.683

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.395 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: 0.349 AC: 52941 AN: 151772 Hom.: 9590 Cov.: 31

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.349 AC: 52968 AN: 151890 Hom.: 9599 Cov.: 31 AF XY: 0.353 AC XY: 26185 AN XY: 74234

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.374

Gnomad4 ASJ AF: 0.315

Gnomad4 EAS AF: 0.410

Gnomad4 SAS AF: 0.355

Gnomad4 FIN AF: 0.479

Gnomad4 NFE AF: 0.385

Gnomad4 OTH AF: 0.349

Alfa AF: 0.228 Hom.: 538

Bravo AF: 0.337

Asia WGS AF: 0.382 AC: 1326 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.64
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11073742; hg19: chr15-88359293;