rs12650031

Variant names:

• chr4-117876678-C-T
• rs12650031
• ENST00000767785.1:n.197-14558G>A

Variant summary

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

The ENST00000767785.1(ENSG00000299982):​n.197-14558G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.5 in 151,722 control chromosomes in the GnomAD database, including 21,739 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 0.50 (21739 hom., cov: 32)
• Consequence: ENSG00000299982 ENST00000767785.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56
• Publications: 2 publications found

Genes affected

ENSG00000299982 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.783 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299982	ENST00000767785.1	n.197-14558G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.500 AC: 75737 AN: 151604 Hom.: 21691 Cov.: 32

Gnomad AFR AF: 0.789

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.668

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.590

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.500 AC: 75847 AN: 151722 Hom.: 21739 Cov.: 32 AF XY: 0.504 AC XY: 37387 AN XY: 74150

African (AFR) AF: 0.790 AC: 32717 AN: 41424

American (AMR) AF: 0.461 AC: 7020 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.460 AC: 1591 AN: 3460

East Asian (EAS) AF: 0.667 AC: 3412 AN: 5116

South Asian (SAS) AF: 0.388 AC: 1866 AN: 4806

European-Finnish (FIN) AF: 0.415 AC: 4386 AN: 10560

Middle Eastern (MID) AF: 0.600 AC: 174 AN: 290

European-Non Finnish (NFE) AF: 0.342 AC: 23216 AN: 67828

Other (OTH) AF: 0.520 AC: 1099 AN: 2112

Alfa AF: 0.411 Hom.: 5602

Bravo AF: 0.523

Asia WGS AF: 0.513 AC: 1782 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.0050
DANN	Benign	0.42
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs12650031; hg19: chr4-118797833;