rs10498719

Variant names:

• chr6-23647806-C-T
• rs10498719

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 0.168 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
• Publications: 1 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 (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

African (AFR) AF: 0.176 AC: 7293 AN: 41430

American (AMR) AF: 0.144 AC: 2207 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 392 AN: 3468

East Asian (EAS) AF: 0.152 AC: 787 AN: 5168

South Asian (SAS) AF: 0.158 AC: 761 AN: 4824

European-Finnish (FIN) AF: 0.141 AC: 1492 AN: 10582

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.178 AC: 12109 AN: 67974

Other (OTH) AF: 0.164 AC: 347 AN: 2110

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
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs10498719; hg19: chr6-23648034;