rs10498902

chr6-74768915-G-A

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 0.0138 in 152,274 control chromosomes in the GnomAD database, including 102 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 0.014 (102 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.452

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.128 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: 0.0139 AC: 2112 AN: 152156 Hom.: 102 Cov.: 32

Gnomad AFR AF: 0.00125

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0365

Gnomad ASJ AF: 0.00202

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.0741

Gnomad FIN AF: 0.00499

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.00482

Gnomad OTH AF: 0.0191

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

GnomAD4 genome AF: 0.0138 AC: 2108 AN: 152274 Hom.: 102 Cov.: 32 AF XY: 0.0166 AC XY: 1237 AN XY: 74450

Gnomad4 AFR AF: 0.00125

Gnomad4 AMR AF: 0.0364

Gnomad4 ASJ AF: 0.00202

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.0740

Gnomad4 FIN AF: 0.00499

Gnomad4 NFE AF: 0.00482

Gnomad4 OTH AF: 0.0194

Alfa AF: 0.00672 Hom.: 4

Bravo AF: 0.0145

Asia WGS AF: 0.0990 AC: 343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	4.7
Dann	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10498902; hg19: chr6-75478631;