rs11072158

Positions:

• chr15-70342370-A-C
• chr15-70342370-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0164 in 152,048 control chromosomes in the GnomAD database, including 33 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 0.016 (33 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0164 (2488/152048) while in subpopulation NFE AF= 0.0226 (1537/67998). AF 95% confidence interval is 0.0217. There are 33 homozygotes in gnomad4. There are 1207 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 33 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0164 AC: 2489 AN: 151930 Hom.: 33 Cov.: 31

Gnomad AFR AF: 0.00431

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0109

Gnomad ASJ AF: 0.0435

Gnomad EAS AF: 0.00310

Gnomad SAS AF: 0.0228

Gnomad FIN AF: 0.0256

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0226

Gnomad OTH AF: 0.0168

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

GnomAD4 genome AF: 0.0164 AC: 2488 AN: 152048 Hom.: 33 Cov.: 31 AF XY: 0.0162 AC XY: 1207 AN XY: 74354

Gnomad4 AFR AF: 0.00430

Gnomad4 AMR AF: 0.0109

Gnomad4 ASJ AF: 0.0435

Gnomad4 EAS AF: 0.00311

Gnomad4 SAS AF: 0.0224

Gnomad4 FIN AF: 0.0256

Gnomad4 NFE AF: 0.0226

Gnomad4 OTH AF: 0.0166

Alfa AF: 0.00986 Hom.: 2285

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.15
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11072158; hg19: chr15-70634709;