rs10500247

Variant names:

• chr19-31042330-A-G
• rs10500247

Your query was ambiguous. Multiple possible variants found:

• chr19-31042330-A-G
• chr19-31042330-A-T

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 0.055 in 152,290 control chromosomes in the GnomAD database, including 644 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 0.055 (644 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.607

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.171 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: 0.0546 AC: 8311 AN: 152172 Hom.: 627 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.0835

Gnomad AMR AF: 0.0229

Gnomad ASJ AF: 0.00893

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0273

Gnomad FIN AF: 0.00640

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00591

Gnomad OTH AF: 0.0388

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

GnomAD4 genome AF: 0.0550 AC: 8369 AN: 152290 Hom.: 644 Cov.: 32 AF XY: 0.0541 AC XY: 4030 AN XY: 74484

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.0229

Gnomad4 ASJ AF: 0.00893

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0274

Gnomad4 FIN AF: 0.00640

Gnomad4 NFE AF: 0.00591

Gnomad4 OTH AF: 0.0384

Alfa AF: 0.00795 Hom.: 11

Bravo AF: 0.0597

Asia WGS AF: 0.0270 AC: 92 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.38
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10500247; hg19: chr19-31533236;