rs36212119

Variant names:

• chr1-32291652-T-C
• rs36212119

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 0.0523 in 152,258 control chromosomes in the GnomAD database, including 266 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 0.052 (266 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.645

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0752 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: 0.0524 AC: 7970 AN: 152140 Hom.: 266 Cov.: 31

Gnomad AFR AF: 0.0152

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.0605

Gnomad ASJ AF: 0.0501

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0155

Gnomad FIN AF: 0.0617

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0769

Gnomad OTH AF: 0.0650

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

GnomAD4 genome AF: 0.0523 AC: 7965 AN: 152258 Hom.: 266 Cov.: 31 AF XY: 0.0501 AC XY: 3731 AN XY: 74438

Gnomad4 AFR AF: 0.0151

Gnomad4 AMR AF: 0.0603

Gnomad4 ASJ AF: 0.0501

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0153

Gnomad4 FIN AF: 0.0617

Gnomad4 NFE AF: 0.0769

Gnomad4 OTH AF: 0.0639

Alfa AF: 0.0659 Hom.: 68

Bravo AF: 0.0512

Asia WGS AF: 0.0110 AC: 38 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.6
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs36212119; hg19: chr1-32757253; COSMIC: COSV65190714;