rs10498719

Positions:

• chr6-23647806-C-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 0.168 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;