4-188665925-C-T

Position:

• chr4-188665925-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.162 in 151,948 control chromosomes in the GnomAD database, including 2,068 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 0.16 (2068 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.415

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.188665925C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01060	ENST00000503580.1	n.88-14796C>T		intron_variant		3
LINC01060	ENST00000664177.1	n.331-14358C>T		intron_variant
LINC01060	ENST00000692519.1	n.362-14358C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24654 AN: 151830 Hom.: 2065 Cov.: 32

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.0828

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.162 AC: 24678 AN: 151948 Hom.: 2068 Cov.: 32 AF XY: 0.157 AC XY: 11683 AN XY: 74278

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.0828

Gnomad4 EAS AF: 0.107

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.170

Alfa AF: 0.158 Hom.: 4242

Bravo AF: 0.162

Asia WGS AF: 0.117 AC: 407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.3
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7659062; hg19: chr4-189587079;