rs4802100

Variant names:

• chr19-40990120-C-G
• rs4802100

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 0.093 in 152,152 control chromosomes in the GnomAD database, including 884 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 0.093 (884 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.522
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.161 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: 0.0930 AC: 14139 AN: 152034 Hom.: 879 Cov.: 31

Gnomad AFR AF: 0.0419

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.0874

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0938

Gnomad OTH AF: 0.0926

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

GnomAD4 genome AF: 0.0930 AC: 14149 AN: 152152 Hom.: 884 Cov.: 31 AF XY: 0.0978 AC XY: 7277 AN XY: 74370

African (AFR) AF: 0.0419 AC: 1739 AN: 41496

American (AMR) AF: 0.153 AC: 2336 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0874 AC: 303 AN: 3468

East Asian (EAS) AF: 0.171 AC: 882 AN: 5170

South Asian (SAS) AF: 0.136 AC: 657 AN: 4820

European-Finnish (FIN) AF: 0.151 AC: 1593 AN: 10584

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0938 AC: 6380 AN: 68020

Other (OTH) AF: 0.0907 AC: 192 AN: 2116

Alfa AF: 0.0999 Hom.: 127

Bravo AF: 0.0918

Asia WGS AF: 0.143 AC: 498 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	0.63
DANN	Benign	0.83
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs4802100; hg19: chr19-41496025;