rs10742326

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.34788463G>A		intergenic_region
LOC102723568	XR_007062652.1	n.1044+33856G>A		intron_variant

Ensembl

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

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

Gnomad4 AFR AF: 0.410

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.326

Gnomad4 EAS AF: 0.428

Gnomad4 SAS AF: 0.367

Gnomad4 FIN AF: 0.442

Gnomad4 NFE AF: 0.414

Gnomad4 OTH AF: 0.376

Alfa AF: 0.408 Hom.: 1538

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

Splicing

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

Publications

LitVar

Other links and lift over

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