rs11239762

Variant names:

• chr10-42766813-G-A
• rs11239762
• ENST00000728931.1:n.557-2466G>A

Variant summary

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

The NR_134498.1(LOC105378269):​n.285-2466G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,078 control chromosomes in the GnomAD database, including 1,091 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 0.11 (1091 hom., cov: 32)
• Consequence: LOC105378269 NR_134498.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 6 publications found

Genes affected

ENSG00000295267 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_134498.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105378269	NR_134498.1		n.285-2466G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000295267	ENST00000728931.1		n.557-2466G>A		intron	N/A
	ENSG00000295267	ENST00000728932.1		n.237-2466G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16735 AN: 151960 Hom.: 1080 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.0253

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0743

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.110 AC: 16770 AN: 152078 Hom.: 1091 Cov.: 32 AF XY: 0.112 AC XY: 8333 AN XY: 74326

African (AFR) AF: 0.176 AC: 7318 AN: 41462

American (AMR) AF: 0.111 AC: 1697 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 444 AN: 3468

East Asian (EAS) AF: 0.0247 AC: 128 AN: 5174

South Asian (SAS) AF: 0.136 AC: 653 AN: 4818

European-Finnish (FIN) AF: 0.113 AC: 1190 AN: 10570

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0743 AC: 5051 AN: 68002

Other (OTH) AF: 0.103 AC: 217 AN: 2108

Alfa AF: 0.0896 Hom.: 400

Bravo AF: 0.113

Asia WGS AF: 0.0960 AC: 334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.99
DANN	Benign	0.67
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs11239762; hg19: chr10-43262261;