rs736289

Variant names:

• chr19-33266156-T-C
• rs736289

Your query was ambiguous. Multiple possible variants found:

• chr19-33266156-T-C
• chr19-33266156-T-G

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 0.462 in 151,932 control chromosomes in the GnomAD database, including 17,479 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 0.46 (17479 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.98
• Publications: 42 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.649 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: 0.462 AC: 70157 AN: 151814 Hom.: 17460 Cov.: 32

Gnomad AFR AF: 0.655

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.462 AC: 70213 AN: 151932 Hom.: 17479 Cov.: 32 AF XY: 0.461 AC XY: 34197 AN XY: 74252

African (AFR) AF: 0.655 AC: 27141 AN: 41434

American (AMR) AF: 0.306 AC: 4676 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.345 AC: 1197 AN: 3468

East Asian (EAS) AF: 0.480 AC: 2462 AN: 5134

South Asian (SAS) AF: 0.457 AC: 2200 AN: 4810

European-Finnish (FIN) AF: 0.420 AC: 4424 AN: 10544

Middle Eastern (MID) AF: 0.445 AC: 130 AN: 292

European-Non Finnish (NFE) AF: 0.395 AC: 26815 AN: 67956

Other (OTH) AF: 0.440 AC: 926 AN: 2106

Alfa AF: 0.412 Hom.: 56069

Bravo AF: 0.461

Asia WGS AF: 0.449 AC: 1565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.021
DANN	Benign	0.30
PhyloP100		-4.0

Splicing

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

Other links and lift over

dbSNP: rs736289; hg19: chr19-33757062;