rs10500242

Variant names:

• chr19-29837679-G-A
• rs10500242

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 0.0438 in 152,330 control chromosomes in the GnomAD database, including 172 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 0.044 (172 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.600
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0503 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: 0.0438 AC: 6667 AN: 152212 Hom.: 172 Cov.: 32

Gnomad AFR AF: 0.0347

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.0529

Gnomad ASJ AF: 0.0821

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0327

Gnomad FIN AF: 0.0262

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0517

Gnomad OTH AF: 0.0415

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

GnomAD4 genome AF: 0.0438 AC: 6665 AN: 152330 Hom.: 172 Cov.: 32 AF XY: 0.0431 AC XY: 3209 AN XY: 74490

African (AFR) AF: 0.0347 AC: 1441 AN: 41586

American (AMR) AF: 0.0529 AC: 809 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0821 AC: 285 AN: 3472

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5180

South Asian (SAS) AF: 0.0328 AC: 158 AN: 4824

European-Finnish (FIN) AF: 0.0262 AC: 278 AN: 10624

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0517 AC: 3517 AN: 68020

Other (OTH) AF: 0.0406 AC: 86 AN: 2116

Alfa AF: 0.0416 Hom.: 58

Bravo AF: 0.0446

Asia WGS AF: 0.0190 AC: 65 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.1
DANN	Benign	0.59
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs10500242; hg19: chr19-30328586;