19-29096562-A-G

Variant names:

• chr19-29096562-A-G
• rs10500237

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 0.0435 in 152,304 control chromosomes in the GnomAD database, including 257 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 0.043 (257 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.188 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: 0.0435 AC: 6623 AN: 152186 Hom.: 258 Cov.: 33

Gnomad AFR AF: 0.0580

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.0360

Gnomad ASJ AF: 0.0496

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.00743

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0232

Gnomad OTH AF: 0.0444

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

GnomAD4 genome AF: 0.0435 AC: 6624 AN: 152304 Hom.: 257 Cov.: 33 AF XY: 0.0454 AC XY: 3381 AN XY: 74472

African (AFR) AF: 0.0579 AC: 2407 AN: 41574

American (AMR) AF: 0.0358 AC: 548 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0496 AC: 172 AN: 3470

East Asian (EAS) AF: 0.198 AC: 1024 AN: 5168

South Asian (SAS) AF: 0.126 AC: 607 AN: 4820

European-Finnish (FIN) AF: 0.00743 AC: 79 AN: 10628

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0232 AC: 1581 AN: 68026

Other (OTH) AF: 0.0501 AC: 106 AN: 2116

Alfa AF: 0.0338 Hom.: 56

Bravo AF: 0.0461

Asia WGS AF: 0.174 AC: 605 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.74
DANN	Benign	0.67
PhyloP100		0.035

Splicing

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

Other links and lift over

dbSNP: rs10500237; hg19: chr19-29587469;