rs36212119

chr1-32291652-T-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 0.0523 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;