rs2346061

Variant names:

• chr18-74533297-C-A
• rs2346061

Your query was ambiguous. Multiple possible variants found:

• chr18-74533297-C-A
• chr18-74533297-C-G

Variant summary

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

The variant allele was found at a frequency of 0.711 in 152,060 control chromosomes in the GnomAD database, including 39,437 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 0.71 (39437 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.304
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.827 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.711 AC: 108080 AN: 151942 Hom.: 39436 Cov.: 32

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.904

Gnomad AMR AF: 0.783

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.848

Gnomad SAS AF: 0.760

Gnomad FIN AF: 0.800

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.769

Gnomad OTH AF: 0.746

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

GnomAD4 genome AF: 0.711 AC: 108118 AN: 152060 Hom.: 39437 Cov.: 32 AF XY: 0.716 AC XY: 53202 AN XY: 74322

African (AFR) AF: 0.532 AC: 22044 AN: 41434

American (AMR) AF: 0.783 AC: 11970 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.779 AC: 2703 AN: 3468

East Asian (EAS) AF: 0.848 AC: 4371 AN: 5156

South Asian (SAS) AF: 0.759 AC: 3659 AN: 4820

European-Finnish (FIN) AF: 0.800 AC: 8454 AN: 10572

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.769 AC: 52287 AN: 68002

Other (OTH) AF: 0.747 AC: 1575 AN: 2108

Alfa AF: 0.754 Hom.: 63784

Bravo AF: 0.706

Asia WGS AF: 0.804 AC: 2790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.66
DANN	Benign	0.61
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs2346061; hg19: chr18-72200532;