rs10738760

Variant names:

• chr9-2691186-A-G
• rs10738760
• XR_929436.3:n.3276T>C

Variant summary

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

The XR_929436.3(LOC105375957):​n.3276T>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 0.555 in 151,956 control chromosomes in the GnomAD database, including 24,348 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 0.56 (24348 hom., cov: 31)
• Consequence: LOC105375957 XR_929436.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51
• Publications: 47 publications found

Genes affected

LOC105375957 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375957	XR_929436.3	n.3276T>C		non_coding_transcript_exon_variant	Exon 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286670	ENST00000768783.1	n.114-23125T>C		intron_variant	Intron 1 of 3
ENSG00000286670	ENST00000768784.1	n.157-23125T>C		intron_variant	Intron 1 of 3
ENSG00000286670	ENST00000768785.1	n.157-26111T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84269 AN: 151838 Hom.: 24301 Cov.: 31

Gnomad AFR AF: 0.713

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.538

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.573

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.555 AC: 84375 AN: 151956 Hom.: 24348 Cov.: 31 AF XY: 0.556 AC XY: 41302 AN XY: 74270

African (AFR) AF: 0.713 AC: 29546 AN: 41448

American (AMR) AF: 0.538 AC: 8221 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1855 AN: 3468

East Asian (EAS) AF: 0.574 AC: 2956 AN: 5154

South Asian (SAS) AF: 0.495 AC: 2375 AN: 4800

European-Finnish (FIN) AF: 0.498 AC: 5258 AN: 10550

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.479 AC: 32535 AN: 67944

Other (OTH) AF: 0.517 AC: 1092 AN: 2112

Alfa AF: 0.502 Hom.: 85642

Bravo AF: 0.563

Asia WGS AF: 0.548 AC: 1905 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.051
DANN	Benign	0.22
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs10738760; hg19: chr9-2691186;