rs10498719

Variant names:

• chr6-23647806-C-T
• rs10498719

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 0.168 in 152,054 control chromosomes in the GnomAD database, including 2,145 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 0.17 (2145 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.38

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.175 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: 0.167 AC: 25446 AN: 151936 Hom.: 2136 Cov.: 33

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.168 AC: 25475 AN: 152054 Hom.: 2145 Cov.: 33 AF XY: 0.165 AC XY: 12236 AN XY: 74316

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.158

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.178

Gnomad4 OTH AF: 0.164

Alfa AF: 0.147 Hom.: 295

Bravo AF: 0.165

Asia WGS AF: 0.214 AC: 748 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	0.11
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10498719; hg19: chr6-23648034;