rs10500264

Variant names:

• chr19-33259408-G-A
• rs10500264

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 0.144 in 152,022 control chromosomes in the GnomAD database, including 1,759 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 0.14 (1759 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0260
• Publications: 35 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.229 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: 0.144 AC: 21899 AN: 151904 Hom.: 1755 Cov.: 32

Gnomad AFR AF: 0.0864

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.0684

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.144 AC: 21907 AN: 152022 Hom.: 1759 Cov.: 32 AF XY: 0.145 AC XY: 10757 AN XY: 74306

African (AFR) AF: 0.0864 AC: 3585 AN: 41480

American (AMR) AF: 0.128 AC: 1949 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 882 AN: 3468

East Asian (EAS) AF: 0.0682 AC: 353 AN: 5176

South Asian (SAS) AF: 0.241 AC: 1159 AN: 4810

European-Finnish (FIN) AF: 0.157 AC: 1659 AN: 10552

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.172 AC: 11723 AN: 67968

Other (OTH) AF: 0.164 AC: 345 AN: 2110

Alfa AF: 0.163 Hom.: 8029

Bravo AF: 0.135

Asia WGS AF: 0.136 AC: 474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.0
DANN	Benign	0.71
PhyloP100		0.026

Splicing

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

Other links and lift over

dbSNP: rs10500264; hg19: chr19-33750314;