rs11072158

Variant names:

• chr15-70342370-A-C
• rs11072158
• ENST00000819859.1:n.630+5488T>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000819859.1(ENSG00000306630):​n.630+5488T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000306630 ENST00000819859.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93
• Publications: 3 publications found

Genes affected

ENSG00000306630 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 33 gene

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
ENSG00000306630	ENST00000819859.1	n.630+5488T>G		intron_variant	Intron 3 of 3
ENSG00000306630	ENST00000819860.1	n.172+5488T>G		intron_variant	Intron 2 of 2
ENSG00000306630	ENST00000819861.1	n.414+5488T>G		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.00430 AC: 178 AN: 41428

American (AMR) AF: 0.0109 AC: 167 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0435 AC: 151 AN: 3472

East Asian (EAS) AF: 0.00311 AC: 16 AN: 5148

South Asian (SAS) AF: 0.0224 AC: 108 AN: 4820

European-Finnish (FIN) AF: 0.0256 AC: 271 AN: 10586

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0226 AC: 1537 AN: 67998

Other (OTH) AF: 0.0166 AC: 35 AN: 2110

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
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs11072158; hg19: chr15-70634709;