rs1901242

Variant names:

• chr12-97636534-G-A
• rs1901242

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 0.193 in 152,004 control chromosomes in the GnomAD database, including 3,248 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 0.19 (3248 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.143

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29325 AN: 151886 Hom.: 3238 Cov.: 32

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.142

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.000965

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.193 AC: 29359 AN: 152004 Hom.: 3248 Cov.: 32 AF XY: 0.187 AC XY: 13885 AN XY: 74298

Gnomad4 AFR AF: 0.293

Gnomad4 AMR AF: 0.158

Gnomad4 ASJ AF: 0.222

Gnomad4 EAS AF: 0.000967

Gnomad4 SAS AF: 0.214

Gnomad4 FIN AF: 0.108

Gnomad4 NFE AF: 0.166

Gnomad4 OTH AF: 0.197

Alfa AF: 0.176 Hom.: 5157

Bravo AF: 0.201

Asia WGS AF: 0.0940 AC: 328 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.5
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1901242; hg19: chr12-98030312;