rs10500242

Positions:

• chr19-29837679-G-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0347

Gnomad4 AMR AF: 0.0529

Gnomad4 ASJ AF: 0.0821

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0328

Gnomad4 FIN AF: 0.0262

Gnomad4 NFE AF: 0.0517

Gnomad4 OTH AF: 0.0406

Alfa AF: 0.0447 Hom.: 22

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10500242; hg19: chr19-30328586;