10-31606911-C-T

Variant names:

• chr10-31606911-C-T
• rs1016836
• XR_930803.3:n.3665G>A

Variant summary

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

The XR_930803.3(LOC105376484):​n.3665G>A 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 0.675 in 152,046 control chromosomes in the GnomAD database, including 34,900 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 0.67 (34900 hom., cov: 32)
• Consequence: LOC105376484 XR_930803.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360
• Publications: 4 publications found

Genes affected

LOC105376484 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376484	XR_930803.3	n.3665G>A		non_coding_transcript_exon_variant	Exon 3 of 3
LOC105376484	XR_930804.3	n.3600G>A		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: 0.675 AC: 102534 AN: 151924 Hom.: 34864 Cov.: 32

Gnomad AFR AF: 0.687

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.672

Gnomad EAS AF: 0.414

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.665

Gnomad MID AF: 0.704

Gnomad NFE AF: 0.695

Gnomad OTH AF: 0.657

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

GnomAD4 genome AF: 0.675 AC: 102623 AN: 152046 Hom.: 34900 Cov.: 32 AF XY: 0.670 AC XY: 49816 AN XY: 74314

African (AFR) AF: 0.687 AC: 28457 AN: 41434

American (AMR) AF: 0.684 AC: 10450 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.672 AC: 2331 AN: 3468

East Asian (EAS) AF: 0.414 AC: 2140 AN: 5170

South Asian (SAS) AF: 0.577 AC: 2781 AN: 4820

European-Finnish (FIN) AF: 0.665 AC: 7031 AN: 10570

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.695 AC: 47253 AN: 67990

Other (OTH) AF: 0.655 AC: 1380 AN: 2108

Alfa AF: 0.685 Hom.: 20981

Bravo AF: 0.680

Asia WGS AF: 0.465 AC: 1622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.3
DANN	Benign	0.55
PhyloP100		-0.036

Splicing

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

Other links and lift over

dbSNP: rs1016836; hg19: chr10-31895839;