rs1797404

chr12-66186298-G-Achr12-66186298-G-T

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 0.24 in 151,656 control chromosomes in the GnomAD database, including 6,343 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 0.24 (6343 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.158

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 (AFR) allele frequency at 95% confidence interval = 0.469 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: 0.240 AC: 36384 AN: 151540 Hom.: 6330 Cov.: 30

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.240 AC: 36440 AN: 151656 Hom.: 6343 Cov.: 30 AF XY: 0.241 AC XY: 17870 AN XY: 74130

Gnomad4 AFR AF: 0.474

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.467

Gnomad4 SAS AF: 0.242

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.211

Alfa AF: 0.145 Hom.: 2449

Bravo AF: 0.250

Asia WGS AF: 0.365 AC: 1264 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	2.6
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1797404; hg19: chr12-66580078;