rs1994641

Variant names:

• chr12-18920410-G-A
• rs1994641

Your query was ambiguous. Multiple possible variants found:

• chr12-18920410-G-A
• chr12-18920410-G-C

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 0.802 in 152,006 control chromosomes in the GnomAD database, including 50,030 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 0.80 (50030 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.274
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.892 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: 0.802 AC: 121804 AN: 151888 Hom.: 49995 Cov.: 31

Gnomad AFR AF: 0.607

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.867

Gnomad ASJ AF: 0.772

Gnomad EAS AF: 0.913

Gnomad SAS AF: 0.903

Gnomad FIN AF: 0.884

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.878

Gnomad OTH AF: 0.813

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

GnomAD4 genome AF: 0.802 AC: 121888 AN: 152006 Hom.: 50030 Cov.: 31 AF XY: 0.803 AC XY: 59662 AN XY: 74304

African (AFR) AF: 0.607 AC: 25150 AN: 41416

American (AMR) AF: 0.868 AC: 13230 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.772 AC: 2680 AN: 3472

East Asian (EAS) AF: 0.913 AC: 4718 AN: 5166

South Asian (SAS) AF: 0.903 AC: 4352 AN: 4820

European-Finnish (FIN) AF: 0.884 AC: 9346 AN: 10574

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.878 AC: 59731 AN: 67994

Other (OTH) AF: 0.814 AC: 1720 AN: 2112

Alfa AF: 0.773 Hom.: 1912

Bravo AF: 0.790

Asia WGS AF: 0.899 AC: 3125 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.56
DANN	Benign	0.21
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs1994641; hg19: chr12-19073344;