rs10498842

Variant names:

• chr6-65985012-T-C
• rs10498842

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 0.106 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0223 AC: 926 AN: 41546

American (AMR) AF: 0.147 AC: 2235 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 511 AN: 3470

East Asian (EAS) AF: 0.132 AC: 679 AN: 5162

South Asian (SAS) AF: 0.165 AC: 796 AN: 4824

European-Finnish (FIN) AF: 0.180 AC: 1898 AN: 10570

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8788 AN: 67944

Other (OTH) AF: 0.0968 AC: 204 AN: 2108

Alfa AF: 0.120 Hom.: 1451

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
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs10498842; hg19: chr6-66694905;