rs36212119

Variant names:

• chr1-32291652-T-C
• rs36212119

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0151 AC: 628 AN: 41558

American (AMR) AF: 0.0603 AC: 922 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0501 AC: 174 AN: 3470

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5182

South Asian (SAS) AF: 0.0153 AC: 74 AN: 4826

European-Finnish (FIN) AF: 0.0617 AC: 654 AN: 10602

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0769 AC: 5231 AN: 68018

Other (OTH) AF: 0.0639 AC: 135 AN: 2114

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
PhyloP100		-0.65
PromoterAI		-0.035	Neutral

Splicing

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

Other links and lift over

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