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

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.

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: 0.135 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

Gnomad4 AFR AF: 0.0498 AC: 0.049834 AN: 0.049834

Gnomad4 AMR AF: 0.106 AC: 0.106414 AN: 0.106414

Gnomad4 ASJ AF: 0.129 AC: 0.12932 AN: 0.12932

Gnomad4 EAS AF: 0.163 AC: 0.162543 AN: 0.162543

Gnomad4 SAS AF: 0.211 AC: 0.210996 AN: 0.210996

Gnomad4 FIN AF: 0.254 AC: 0.25417 AN: 0.25417

Gnomad4 NFE AF: 0.167 AC: 0.167349 AN: 0.167349

Gnomad4 OTH AF: 0.131 AC: 0.13138 AN: 0.13138

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4466060; hg19: chr4-131582321;