rs4128664

Variant names:

• chr10-46332377-C-T
• rs4128664

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 0.451 in 151,744 control chromosomes in the GnomAD database, including 15,414 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 0.45 (15414 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.493
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68319 AN: 151626 Hom.: 15397 Cov.: 33

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.451 AC: 68385 AN: 151744 Hom.: 15414 Cov.: 33 AF XY: 0.448 AC XY: 33256 AN XY: 74160

African (AFR) AF: 0.518 AC: 21438 AN: 41352

American (AMR) AF: 0.500 AC: 7614 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.432 AC: 1498 AN: 3464

East Asian (EAS) AF: 0.121 AC: 625 AN: 5176

South Asian (SAS) AF: 0.299 AC: 1440 AN: 4812

European-Finnish (FIN) AF: 0.471 AC: 4960 AN: 10528

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.433 AC: 29405 AN: 67860

Other (OTH) AF: 0.432 AC: 912 AN: 2112

Alfa AF: 0.435 Hom.: 13061

Asia WGS AF: 0.245 AC: 856 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.59
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs4128664; hg19: chr10-47703613;