rs10485351

Variant names:

• chr6-167783678-G-A
• rs10485351

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 0.127 in 152,200 control chromosomes in the GnomAD database, including 1,646 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 0.13 (1646 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.447

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.183 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: 0.127 AC: 19303 AN: 152082 Hom.: 1649 Cov.: 33

Gnomad AFR AF: 0.0339

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.0135

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.127 AC: 19296 AN: 152200 Hom.: 1646 Cov.: 33 AF XY: 0.123 AC XY: 9182 AN XY: 74412

Gnomad4 AFR AF: 0.0338 AC: 0.0337555 AN: 0.0337555

Gnomad4 AMR AF: 0.119 AC: 0.119101 AN: 0.119101

Gnomad4 ASJ AF: 0.213 AC: 0.212514 AN: 0.212514

Gnomad4 EAS AF: 0.0133 AC: 0.0133102 AN: 0.0133102

Gnomad4 SAS AF: 0.130 AC: 0.130336 AN: 0.130336

Gnomad4 FIN AF: 0.145 AC: 0.145152 AN: 0.145152

Gnomad4 NFE AF: 0.185 AC: 0.185478 AN: 0.185478

Gnomad4 OTH AF: 0.144 AC: 0.144076 AN: 0.144076

Alfa AF: 0.157 Hom.: 3622

Bravo AF: 0.123

Asia WGS AF: 0.0740 AC: 257 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.40
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10485351; hg19: chr6-168184358;