rs2981004

Variant names:

• chr18-62313302-G-A
• rs2981004
• ENST00000756986.1:n.250+10066C>T

Your query was ambiguous. Multiple possible variants found:

• chr18-62313302-G-A
• chr18-62313302-G-C

Variant summary

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

The ENST00000756986.1(ENSG00000267560):​n.250+10066C>T 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 152,058 control chromosomes in the GnomAD database, including 40,098 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 (40098 hom., cov: 32)
• Consequence: ENSG00000267560 ENST00000756986.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.569
• Publications: 8 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.875 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000756986.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000267560	ENST00000756986.1		n.250+10066C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.723 AC: 109901 AN: 151940 Hom.: 40062 Cov.: 32

Gnomad AFR AF: 0.648

Gnomad AMI AF: 0.699

Gnomad AMR AF: 0.774

Gnomad ASJ AF: 0.768

Gnomad EAS AF: 0.897

Gnomad SAS AF: 0.834

Gnomad FIN AF: 0.748

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.730

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: 109991 AN: 152058 Hom.: 40098 Cov.: 32 AF XY: 0.728 AC XY: 54078 AN XY: 74332

African (AFR) AF: 0.649 AC: 26873 AN: 41436

American (AMR) AF: 0.774 AC: 11835 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.768 AC: 2666 AN: 3470

East Asian (EAS) AF: 0.897 AC: 4638 AN: 5172

South Asian (SAS) AF: 0.835 AC: 4028 AN: 4824

European-Finnish (FIN) AF: 0.748 AC: 7907 AN: 10566

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

European-Non Finnish (NFE) AF: 0.730 AC: 49659 AN: 67982

Other (OTH) AF: 0.723 AC: 1527 AN: 2112

Alfa AF: 0.719 Hom.: 6620

Bravo AF: 0.722

Asia WGS AF: 0.832 AC: 2893 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.54
DANN	Benign	0.42
PhyloP100		-0.57

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2981004;

hg19: chr18-59980535;