rs10508796

Variant names:

• chr10-34047269-G-A
• rs10508796
• ENST00000726133.1:n.239+28611G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-34047269-G-A
• chr10-34047269-G-T

Variant summary

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

The ENST00000726133.1(ENSG00000288987):​n.239+28611G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 152,004 control chromosomes in the GnomAD database, including 3,129 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 0.12 (3129 hom., cov: 32)
• Consequence: ENSG00000288987 ENST00000726133.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.105
• Publications: 1 publications found

Genes affected

ENSG00000288987 (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 (AFR) allele frequency at 95% confidence interval = 0.381 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
ENSG00000288987	ENST00000726133.1	n.239+28611G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17490 AN: 151886 Hom.: 3116 Cov.: 32

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0459

Gnomad ASJ AF: 0.00317

Gnomad EAS AF: 0.000387

Gnomad SAS AF: 0.00436

Gnomad FIN AF: 0.00397

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.00869

Gnomad OTH AF: 0.0910

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

GnomAD4 genome AF: 0.115 AC: 17540 AN: 152004 Hom.: 3129 Cov.: 32 AF XY: 0.112 AC XY: 8294 AN XY: 74310

African (AFR) AF: 0.386 AC: 15965 AN: 41374

American (AMR) AF: 0.0458 AC: 700 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.00317 AC: 11 AN: 3468

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5162

South Asian (SAS) AF: 0.00395 AC: 19 AN: 4814

European-Finnish (FIN) AF: 0.00397 AC: 42 AN: 10586

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.00869 AC: 591 AN: 68006

Other (OTH) AF: 0.0900 AC: 190 AN: 2110

Alfa AF: 0.0656 Hom.: 975

Bravo AF: 0.131

Asia WGS AF: 0.0280 AC: 99 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	13
DANN	Benign	0.38
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs10508796; hg19: chr10-34336197;