11-39215482-A-G

Variant names:

• chr11-39215482-A-G
• rs2035693
• ENST00000722823.1:n.496-29580A>G

Variant summary

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

The ENST00000722823.1(ENSG00000294334):​n.496-29580A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.57 in 151,920 control chromosomes in the GnomAD database, including 25,691 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 0.57 (25691 hom., cov: 32)
• Consequence: ENSG00000294334 ENST00000722823.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141
• Publications: 2 publications found

Genes affected

ENSG00000294334 (HGNC:):

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 = 0.739 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
ENSG00000294334	ENST00000722823.1	n.496-29580A>G		intron_variant	Intron 2 of 3
ENSG00000294334	ENST00000722824.1	n.208-29580A>G		intron_variant	Intron 2 of 4
ENSG00000294334	ENST00000722825.1	n.249-29580A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.570 AC: 86587 AN: 151802 Hom.: 25671 Cov.: 32

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.713

Gnomad AMR AF: 0.672

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.624

Gnomad FIN AF: 0.531

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.570 AC: 86644 AN: 151920 Hom.: 25691 Cov.: 32 AF XY: 0.574 AC XY: 42595 AN XY: 74252

African (AFR) AF: 0.398 AC: 16498 AN: 41462

American (AMR) AF: 0.673 AC: 10271 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.664 AC: 2304 AN: 3468

East Asian (EAS) AF: 0.759 AC: 3919 AN: 5166

South Asian (SAS) AF: 0.626 AC: 3020 AN: 4824

European-Finnish (FIN) AF: 0.531 AC: 5604 AN: 10558

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.632 AC: 42908 AN: 67858

Other (OTH) AF: 0.610 AC: 1287 AN: 2110

Alfa AF: 0.447 Hom.: 1350

Bravo AF: 0.574

Asia WGS AF: 0.695 AC: 2409 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.38
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs2035693; hg19: chr11-39237032;