rs1994641

Positions:

• chr12-18920410-G-A
• chr12-18920410-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 0.802 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.802 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

Gnomad4 AFR AF: 0.607

Gnomad4 AMR AF: 0.868

Gnomad4 ASJ AF: 0.772

Gnomad4 EAS AF: 0.913

Gnomad4 SAS AF: 0.903

Gnomad4 FIN AF: 0.884

Gnomad4 NFE AF: 0.878

Gnomad4 OTH AF: 0.814

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1994641; hg19: chr12-19073344;