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.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

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 v4.9

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;