rs10742326

Variant names:

• chr11-34788463-G-A
• rs10742326
• ENST00000843048.1:n.656+33856G>A

Your query was ambiguous. Multiple possible variants found:

• chr11-34788463-G-A
• chr11-34788463-G-T

Variant summary

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

The ENST00000843048.1(ENSG00000309692):​n.656+33856G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.403 in 151,942 control chromosomes in the GnomAD database, including 12,488 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 0.40 (12488 hom., cov: 31)
• Consequence: ENSG00000309692 ENST00000843048.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 11 publications found

Genes affected

ENSG00000309692 (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 = 0.413 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723568	XR_007062652.1	n.1044+33856G>A		intron_variant	Intron 6 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309692	ENST00000843048.1	n.656+33856G>A		intron_variant	Intron 2 of 2
ENSG00000309692	ENST00000843049.1	n.848+33856G>A		intron_variant	Intron 3 of 3
ENSG00000309692	ENST00000843050.1	n.440+33856G>A		intron_variant	Intron 3 of 3
ENSG00000309692	ENST00000843051.1	n.298+33856G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.403 AC: 61249 AN: 151824 Hom.: 12477 Cov.: 31

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.403 AC: 61289 AN: 151942 Hom.: 12488 Cov.: 31 AF XY: 0.402 AC XY: 29876 AN XY: 74270

African (AFR) AF: 0.410 AC: 16978 AN: 41426

American (AMR) AF: 0.335 AC: 5113 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1131 AN: 3470

East Asian (EAS) AF: 0.428 AC: 2207 AN: 5154

South Asian (SAS) AF: 0.367 AC: 1762 AN: 4806

European-Finnish (FIN) AF: 0.442 AC: 4663 AN: 10546

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.414 AC: 28109 AN: 67946

Other (OTH) AF: 0.376 AC: 794 AN: 2112

Alfa AF: 0.402 Hom.: 3573

Bravo AF: 0.395

Asia WGS AF: 0.399 AC: 1385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.6
DANN	Benign	0.67
PhyloP100		0.0

Splicing

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

Other links and lift over

dbSNP: rs10742326; hg19: chr11-34810010; COSMIC: COSV64822425;