19-33367307-G-C

Variant names:

• chr19-33367307-G-C
• rs736682

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 0.528 in 151,932 control chromosomes in the GnomAD database, including 21,414 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 0.53 (21414 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.995
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.581 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: 0.528 AC: 80155 AN: 151814 Hom.: 21394 Cov.: 31

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.528 AC: 80216 AN: 151932 Hom.: 21414 Cov.: 31 AF XY: 0.526 AC XY: 39031 AN XY: 74266

African (AFR) AF: 0.587 AC: 24315 AN: 41426

American (AMR) AF: 0.519 AC: 7914 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1712 AN: 3472

East Asian (EAS) AF: 0.396 AC: 2039 AN: 5146

South Asian (SAS) AF: 0.373 AC: 1798 AN: 4818

European-Finnish (FIN) AF: 0.534 AC: 5636 AN: 10546

Middle Eastern (MID) AF: 0.517 AC: 150 AN: 290

European-Non Finnish (NFE) AF: 0.517 AC: 35116 AN: 67956

Other (OTH) AF: 0.534 AC: 1126 AN: 2110

Alfa AF: 0.367 Hom.: 913

Bravo AF: 0.534

Asia WGS AF: 0.371 AC: 1292 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.47
DANN	Benign	0.77
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs736682; hg19: chr19-33858213;