chr3-36814539-T-C

Variant names:

• chr3-36814539-T-C
• rs9834970

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 0.45 in 152,054 control chromosomes in the GnomAD database, including 16,143 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 0.45 (16143 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.712
• Publications: 72 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.587 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: 0.451 AC: 68455 AN: 151936 Hom.: 16130 Cov.: 32

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.604

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.450 AC: 68497 AN: 152054 Hom.: 16143 Cov.: 32 AF XY: 0.450 AC XY: 33430 AN XY: 74330

African (AFR) AF: 0.315 AC: 13042 AN: 41454

American (AMR) AF: 0.558 AC: 8521 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.487 AC: 1691 AN: 3470

East Asian (EAS) AF: 0.605 AC: 3124 AN: 5164

South Asian (SAS) AF: 0.528 AC: 2549 AN: 4824

European-Finnish (FIN) AF: 0.392 AC: 4142 AN: 10568

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.497 AC: 33802 AN: 67978

Other (OTH) AF: 0.468 AC: 986 AN: 2106

Alfa AF: 0.487 Hom.: 59046

Bravo AF: 0.455

Asia WGS AF: 0.546 AC: 1897 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	3.2
DANN	Benign	0.73
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs9834970; hg19: chr3-36856030;