chr9-31836557-T-C

Variant names:

• chr9-31836557-T-C
• rs10511886
• XR_929549.2:n.361A>G

Variant summary

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

The XR_929549.2(LOC105376013):​n.361A>G 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 0.556 in 151,618 control chromosomes in the GnomAD database, including 24,525 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 (24525 hom., cov: 29)
• Consequence: LOC105376013 XR_929549.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.322
• Publications: 3 publications found

Genes affected

LOC105376013 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.629 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376013	XR_929549.2	n.361A>G		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84262 AN: 151500 Hom.: 24511 Cov.: 29

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.836

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.628

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.634

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.556 AC: 84322 AN: 151618 Hom.: 24525 Cov.: 29 AF XY: 0.560 AC XY: 41442 AN XY: 74048

African (AFR) AF: 0.378 AC: 15627 AN: 41322

American (AMR) AF: 0.551 AC: 8391 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.627 AC: 2175 AN: 3468

East Asian (EAS) AF: 0.557 AC: 2846 AN: 5114

South Asian (SAS) AF: 0.628 AC: 3020 AN: 4806

European-Finnish (FIN) AF: 0.671 AC: 7069 AN: 10532

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.634 AC: 42997 AN: 67854

Other (OTH) AF: 0.587 AC: 1232 AN: 2098

Alfa AF: 0.611 Hom.: 119612

Bravo AF: 0.536

Asia WGS AF: 0.599 AC: 2082 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.7
DANN	Benign	0.56
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs10511886; hg19: chr9-31836555; COSMIC: COSV60351392;