rs1016836

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.

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: 0.675 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 v4.9

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;