9-2691186-A-G

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000768783.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286670	ENST00000768783.1		n.114-23125T>C		intron	N/A
	ENSG00000286670	ENST00000768784.1		n.157-23125T>C		intron	N/A
	ENSG00000286670	ENST00000768785.1		n.157-26111T>C		intron	N/A

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 v4.9

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;