rs10751635

Variant names:

• chr11-1062990-A-G
• rs10751635
• XR_001748091.2:n.870T>C

Your query was ambiguous. Multiple possible variants found:

• chr11-1062990-A-G
• chr11-1062990-A-T

Variant summary

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

The XR_001748091.2(LOC107987157):​n.870T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 151,726 control chromosomes in the GnomAD database, including 12,636 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 0.41 (12636 hom., cov: 32)
• Consequence: LOC107987157 XR_001748091.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.109
• Publications: 4 publications found

Genes affected

LOC107987157 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000782977.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301936	ENST00000782977.1		n.763-114T>C		intron	N/A
	ENSG00000301936	ENST00000782978.1		n.*32T>C		downstream_gene	N/A
	ENSG00000301936	ENST00000782979.1		n.*33T>C		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61679 AN: 151606 Hom.: 12614 Cov.: 32

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.450

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.407 AC: 61734 AN: 151726 Hom.: 12636 Cov.: 32 AF XY: 0.404 AC XY: 29961 AN XY: 74150

African (AFR) AF: 0.363 AC: 15019 AN: 41384

American (AMR) AF: 0.337 AC: 5140 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.525 AC: 1815 AN: 3456

East Asian (EAS) AF: 0.393 AC: 2024 AN: 5154

South Asian (SAS) AF: 0.515 AC: 2471 AN: 4798

European-Finnish (FIN) AF: 0.396 AC: 4161 AN: 10514

Middle Eastern (MID) AF: 0.449 AC: 131 AN: 292

European-Non Finnish (NFE) AF: 0.437 AC: 29686 AN: 67858

Other (OTH) AF: 0.417 AC: 879 AN: 2108

Alfa AF: 0.425 Hom.: 36243

Bravo AF: 0.394

Asia WGS AF: 0.431 AC: 1499 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	5.6
DANN	Benign	0.53
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs10751635; hg19: chr11-1062990;