15-31471406-T-G

Variant names:

• chr15-31471406-T-G
• rs11071075
• ENST00000833720.1:n.159-1696T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000833720.1(ENSG00000308379):​n.159-1696T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 152,048 control chromosomes in the GnomAD database, including 5,489 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 0.26 (5489 hom., cov: 32)
• Consequence: ENSG00000308379 ENST00000833720.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.287
• Publications: 3 publications found

Genes affected

ENSG00000308379 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.406 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
ENSG00000308379	ENST00000833720.1	n.159-1696T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38841 AN: 151930 Hom.: 5486 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.256 AC: 38854 AN: 152048 Hom.: 5489 Cov.: 32 AF XY: 0.255 AC XY: 18981 AN XY: 74338

African (AFR) AF: 0.133 AC: 5520 AN: 41466

American (AMR) AF: 0.328 AC: 5011 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1241 AN: 3466

East Asian (EAS) AF: 0.421 AC: 2172 AN: 5164

South Asian (SAS) AF: 0.204 AC: 984 AN: 4822

European-Finnish (FIN) AF: 0.262 AC: 2767 AN: 10562

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.298 AC: 20243 AN: 67966

Other (OTH) AF: 0.275 AC: 581 AN: 2114

Alfa AF: 0.252 Hom.: 1781

Bravo AF: 0.264

Asia WGS AF: 0.314 AC: 1090 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.51
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs11071075; hg19: chr15-31763609;