rs10485285

Variant names:

• chr6-80768890-G-A
• rs10485285

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 0.375 in 151,812 control chromosomes in the GnomAD database, including 10,999 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 0.37 (10999 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0270
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.503 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: 0.375 AC: 56817 AN: 151694 Hom.: 10974 Cov.: 31

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.332

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.375 AC: 56901 AN: 151812 Hom.: 10999 Cov.: 31 AF XY: 0.380 AC XY: 28169 AN XY: 74182

African (AFR) AF: 0.427 AC: 17663 AN: 41396

American (AMR) AF: 0.252 AC: 3832 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1176 AN: 3464

East Asian (EAS) AF: 0.481 AC: 2466 AN: 5128

South Asian (SAS) AF: 0.520 AC: 2505 AN: 4814

European-Finnish (FIN) AF: 0.413 AC: 4349 AN: 10538

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.350 AC: 23805 AN: 67930

Other (OTH) AF: 0.341 AC: 719 AN: 2110

Alfa AF: 0.357 Hom.: 37999

Bravo AF: 0.357

Asia WGS AF: 0.499 AC: 1735 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.3
DANN	Benign	0.50
PhyloP100		0.027

Splicing

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

Other links and lift over

dbSNP: rs10485285; hg19: chr6-81478607;