rs10498842

Positions:

• chr6-65985012-T-C

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 0.106 in 152,078 control chromosomes in the GnomAD database, including 1,107 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 0.11 (1107 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.904

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.156 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: 0.106 AC: 16175 AN: 151960 Hom.: 1109 Cov.: 31

Gnomad AFR AF: 0.0224

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.0973

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

GnomAD4 genome AF: 0.106 AC: 16173 AN: 152078 Hom.: 1107 Cov.: 31 AF XY: 0.111 AC XY: 8281 AN XY: 74326

Gnomad4 AFR AF: 0.0223

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.165

Gnomad4 FIN AF: 0.180

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.0968

Alfa AF: 0.124 Hom.: 1142

Bravo AF: 0.0965

Asia WGS AF: 0.135 AC: 466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.5
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: rs10498842; hg19: chr6-66694905;