rs10738760

Positions:

• chr9-2691186-A-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC105375957 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105375957	XR_929436.3	n.3276T>C		non_coding_transcript_exon_variant	1/3

Ensembl

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

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

Gnomad4 AFR AF: 0.713

Gnomad4 AMR AF: 0.538

Gnomad4 ASJ AF: 0.535

Gnomad4 EAS AF: 0.574

Gnomad4 SAS AF: 0.495

Gnomad4 FIN AF: 0.498

Gnomad4 NFE AF: 0.479

Gnomad4 OTH AF: 0.517

Alfa AF: 0.490 Hom.: 38698

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10738760; hg19: chr9-2691186;