4-130661166-T-C

Variant names:

• chr4-130661166-T-C
• rs4466060

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 0.135 in 152,128 control chromosomes in the GnomAD database, including 1,748 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 0.14 (1748 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.2 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: 0.135 AC: 20589 AN: 152010 Hom.: 1750 Cov.: 32

Gnomad AFR AF: 0.0498

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.135 AC: 20593 AN: 152128 Hom.: 1748 Cov.: 32 AF XY: 0.140 AC XY: 10381 AN XY: 74334

African (AFR) AF: 0.0498 AC: 2071 AN: 41558

American (AMR) AF: 0.106 AC: 1626 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 449 AN: 3472

East Asian (EAS) AF: 0.163 AC: 841 AN: 5174

South Asian (SAS) AF: 0.211 AC: 1017 AN: 4820

European-Finnish (FIN) AF: 0.254 AC: 2682 AN: 10552

Middle Eastern (MID) AF: 0.130 AC: 38 AN: 292

European-Non Finnish (NFE) AF: 0.167 AC: 11372 AN: 67954

Other (OTH) AF: 0.131 AC: 278 AN: 2116

Alfa AF: 0.101 Hom.: 216

Bravo AF: 0.120

Asia WGS AF: 0.156 AC: 543 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.38
DANN	Benign	0.51
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs4466060; hg19: chr4-131582321;