rs1941487

Variant names:

• chr18-6657900-G-A
• rs1941487

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 0.424 in 151,934 control chromosomes in the GnomAD database, including 14,981 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 0.42 (14981 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.528
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.523 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64432 AN: 151818 Hom.: 14963 Cov.: 32

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.424 AC: 64492 AN: 151934 Hom.: 14981 Cov.: 32 AF XY: 0.426 AC XY: 31649 AN XY: 74228

African (AFR) AF: 0.244 AC: 10123 AN: 41408

American (AMR) AF: 0.533 AC: 8138 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.478 AC: 1658 AN: 3470

East Asian (EAS) AF: 0.258 AC: 1334 AN: 5164

South Asian (SAS) AF: 0.436 AC: 2096 AN: 4812

European-Finnish (FIN) AF: 0.535 AC: 5642 AN: 10536

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.502 AC: 34120 AN: 67964

Other (OTH) AF: 0.437 AC: 920 AN: 2106

Alfa AF: 0.483 Hom.: 9969

Bravo AF: 0.412

Asia WGS AF: 0.344 AC: 1203 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.021
DANN	Benign	0.35
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs1941487; hg19: chr18-6657899;