rs36496

Variant names:

• chr19-51458762-C-T
• rs36496

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 0.863 in 152,158 control chromosomes in the GnomAD database, including 57,063 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 0.86 (57063 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.954 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: 0.863 AC: 131151 AN: 152040 Hom.: 57004 Cov.: 31

Gnomad AFR AF: 0.962

Gnomad AMI AF: 0.822

Gnomad AMR AF: 0.882

Gnomad ASJ AF: 0.868

Gnomad EAS AF: 0.880

Gnomad SAS AF: 0.849

Gnomad FIN AF: 0.770

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.812

Gnomad OTH AF: 0.876

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

GnomAD4 genome AF: 0.863 AC: 131272 AN: 152158 Hom.: 57063 Cov.: 31 AF XY: 0.862 AC XY: 64105 AN XY: 74362

African (AFR) AF: 0.962 AC: 39935 AN: 41530

American (AMR) AF: 0.882 AC: 13492 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.868 AC: 3011 AN: 3470

East Asian (EAS) AF: 0.879 AC: 4541 AN: 5164

South Asian (SAS) AF: 0.848 AC: 4086 AN: 4816

European-Finnish (FIN) AF: 0.770 AC: 8145 AN: 10582

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.812 AC: 55210 AN: 67976

Other (OTH) AF: 0.874 AC: 1848 AN: 2114

Alfa AF: 0.830 Hom.: 100112

Bravo AF: 0.876

Asia WGS AF: 0.861 AC: 2995 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.20
PhyloP100		-2.1
PromoterAI		-0.0030	Neutral

Splicing

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

Other links and lift over

dbSNP: rs36496; hg19: chr19-51962016;