3-36032298-G-A

Variant names:

• chr3-36032298-G-A
• rs2198207

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 0.0527 in 152,228 control chromosomes in the GnomAD database, including 465 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 0.053 (465 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.289 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: 0.0527 AC: 8014 AN: 152110 Hom.: 464 Cov.: 32

Gnomad AFR AF: 0.0116

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.0560

Gnomad ASJ AF: 0.0314

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.0972

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0452

Gnomad OTH AF: 0.0536

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

GnomAD4 genome AF: 0.0527 AC: 8021 AN: 152228 Hom.: 465 Cov.: 32 AF XY: 0.0574 AC XY: 4270 AN XY: 74404

African (AFR) AF: 0.0116 AC: 481 AN: 41564

American (AMR) AF: 0.0560 AC: 857 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0314 AC: 109 AN: 3466

East Asian (EAS) AF: 0.302 AC: 1560 AN: 5174

South Asian (SAS) AF: 0.0973 AC: 469 AN: 4820

European-Finnish (FIN) AF: 0.119 AC: 1263 AN: 10580

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0452 AC: 3076 AN: 68016

Other (OTH) AF: 0.0549 AC: 116 AN: 2112

Alfa AF: 0.0427 Hom.: 237

Bravo AF: 0.0483

Asia WGS AF: 0.196 AC: 679 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.030
DANN	Benign	0.48
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs2198207; hg19: chr3-36073790;