chr10-46070933-C-T

Variant names:

• chr10-46070933-C-T
• rs2611489

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 0.549 in 151,954 control chromosomes in the GnomAD database, including 23,078 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 0.55 (23078 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.09
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.576 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.549 AC: 83396 AN: 151836 Hom.: 23069 Cov.: 32

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.549 AC: 83440 AN: 151954 Hom.: 23078 Cov.: 32 AF XY: 0.548 AC XY: 40663 AN XY: 74250

African (AFR) AF: 0.530 AC: 21956 AN: 41416

American (AMR) AF: 0.586 AC: 8957 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.455 AC: 1577 AN: 3468

East Asian (EAS) AF: 0.539 AC: 2786 AN: 5166

South Asian (SAS) AF: 0.423 AC: 2036 AN: 4818

European-Finnish (FIN) AF: 0.614 AC: 6472 AN: 10548

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.559 AC: 37962 AN: 67952

Other (OTH) AF: 0.532 AC: 1124 AN: 2112

Alfa AF: 0.546 Hom.: 12035

Bravo AF: 0.552

Asia WGS AF: 0.484 AC: 1683 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.10
DANN	Benign	0.41
PhyloP100		-4.1

Splicing

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

Other links and lift over

dbSNP: rs2611489; hg19: chr10-51524889;