rs2981004

chr18-62313302-G-Achr18-62313302-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.569

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.649

Gnomad4 AMR AF: 0.774

Gnomad4 ASJ AF: 0.768

Gnomad4 EAS AF: 0.897

Gnomad4 SAS AF: 0.835

Gnomad4 FIN AF: 0.748

Gnomad4 NFE AF: 0.730

Gnomad4 OTH AF: 0.723

Alfa AF: 0.721 Hom.: 6445

Bravo AF: 0.722

Asia WGS AF: 0.832 AC: 2893 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.54
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2981004; hg19: chr18-59980535;