18-62312962-T-C

Variant names:

• chr18-62312962-T-C
• rs2981003
• ENST00000756986.1:n.250+10406A>G

Variant summary

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

The ENST00000756986.1(ENSG00000267560):​n.250+10406A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.723 in 151,546 control chromosomes in the GnomAD database, including 39,946 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 0.72 (39946 hom., cov: 29)
• Consequence: ENSG00000267560 ENST00000756986.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.266
• Publications: 6 publications found

Genes affected

ENSG00000267560 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.875 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
ENSG00000267560	ENST00000756986.1	n.250+10406A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.723 AC: 109510 AN: 151428 Hom.: 39910 Cov.: 29

Gnomad AFR AF: 0.649

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.773

Gnomad ASJ AF: 0.768

Gnomad EAS AF: 0.897

Gnomad SAS AF: 0.834

Gnomad FIN AF: 0.745

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.731

Gnomad OTH AF: 0.722

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

GnomAD4 genome AF: 0.723 AC: 109600 AN: 151546 Hom.: 39946 Cov.: 29 AF XY: 0.727 AC XY: 53806 AN XY: 73984

African (AFR) AF: 0.649 AC: 26750 AN: 41230

American (AMR) AF: 0.773 AC: 11801 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.768 AC: 2663 AN: 3466

East Asian (EAS) AF: 0.897 AC: 4622 AN: 5154

South Asian (SAS) AF: 0.835 AC: 4015 AN: 4810

European-Finnish (FIN) AF: 0.745 AC: 7750 AN: 10400

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.731 AC: 49618 AN: 67916

Other (OTH) AF: 0.723 AC: 1524 AN: 2108

Alfa AF: 0.675 Hom.: 3778

Bravo AF: 0.722

Asia WGS AF: 0.831 AC: 2892 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.6
DANN	Benign	0.37
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs2981003; hg19: chr18-59980195;