19-32556208-A-G

Variant names:

• chr19-32556208-A-G
• rs2868145

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 0.148 in 152,048 control chromosomes in the GnomAD database, including 1,732 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 0.15 (1732 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.457
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.159 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: 0.147 AC: 22408 AN: 151930 Hom.: 1727 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.0800

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.148 AC: 22437 AN: 152048 Hom.: 1732 Cov.: 32 AF XY: 0.143 AC XY: 10621 AN XY: 74346

African (AFR) AF: 0.142 AC: 5899 AN: 41470

American (AMR) AF: 0.125 AC: 1906 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 823 AN: 3468

East Asian (EAS) AF: 0.0805 AC: 416 AN: 5166

South Asian (SAS) AF: 0.109 AC: 528 AN: 4824

European-Finnish (FIN) AF: 0.114 AC: 1205 AN: 10582

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.162 AC: 11005 AN: 67992

Other (OTH) AF: 0.158 AC: 332 AN: 2106

Alfa AF: 0.160 Hom.: 9118

Bravo AF: 0.152

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.0
DANN	Benign	0.28
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs2868145; hg19: chr19-33047114;