4-188644016-C-T

Position:

• chr4-188644016-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 0.189 in 152,068 control chromosomes in the GnomAD database, including 2,793 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 0.19 (2793 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.40

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.188644016C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01060	ENST00000503580.1	n.88-36705C>T		intron_variant		3
LINC01060	ENST00000664177.1	n.331-36267C>T		intron_variant
LINC01060	ENST00000692519.1	n.362-36267C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28637 AN: 151950 Hom.: 2777 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.165

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.189 AC: 28703 AN: 152068 Hom.: 2793 Cov.: 32 AF XY: 0.184 AC XY: 13715 AN XY: 74338

Gnomad4 AFR AF: 0.227

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.143

Gnomad4 EAS AF: 0.100

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.142

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.198

Alfa AF: 0.172 Hom.: 2470

Bravo AF: 0.188

Asia WGS AF: 0.167 AC: 579 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.72
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6834498; hg19: chr4-189565170;