rs10485289

Variant names:

• chr6-49674352-G-A
• rs10485289

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 0.0813 in 151,964 control chromosomes in the GnomAD database, including 1,016 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 0.081 (1016 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.672
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.209 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: 0.0812 AC: 12328 AN: 151846 Hom.: 1010 Cov.: 32

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0452

Gnomad ASJ AF: 0.0525

Gnomad EAS AF: 0.0348

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.0127

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0241

Gnomad OTH AF: 0.0706

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

GnomAD4 genome AF: 0.0813 AC: 12357 AN: 151964 Hom.: 1016 Cov.: 32 AF XY: 0.0795 AC XY: 5905 AN XY: 74276

African (AFR) AF: 0.213 AC: 8814 AN: 41440

American (AMR) AF: 0.0452 AC: 688 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.0525 AC: 182 AN: 3464

East Asian (EAS) AF: 0.0349 AC: 180 AN: 5160

South Asian (SAS) AF: 0.114 AC: 547 AN: 4816

European-Finnish (FIN) AF: 0.0127 AC: 135 AN: 10600

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0241 AC: 1638 AN: 67954

Other (OTH) AF: 0.0732 AC: 154 AN: 2104

Alfa AF: 0.0684 Hom.: 123

Bravo AF: 0.0894

Asia WGS AF: 0.0810 AC: 283 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.4
DANN	Benign	0.69
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs10485289; hg19: chr6-49642065;