rs10498968

Variant names:

• chr6-90374161-C-G
• rs10498968

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 0.209 in 152,058 control chromosomes in the GnomAD database, including 3,548 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 0.21 (3548 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.05

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.241 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: 0.209 AC: 31712 AN: 151940 Hom.: 3537 Cov.: 32

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.0206

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.209 AC: 31740 AN: 152058 Hom.: 3548 Cov.: 32 AF XY: 0.204 AC XY: 15191 AN XY: 74330

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.297

Gnomad4 EAS AF: 0.0207

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.176

Gnomad4 NFE AF: 0.245

Gnomad4 OTH AF: 0.225

Alfa AF: 0.223 Hom.: 486

Bravo AF: 0.204

Asia WGS AF: 0.171 AC: 594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.38
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10498968; hg19: chr6-91083880;