4-102078452-T-C

Position:

• chr4-102078452-T-C

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 0.61 in 152,026 control chromosomes in the GnomAD database, including 28,717 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 0.61 (28717 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.538

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.671 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.102078452T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.610 AC: 92637 AN: 151908 Hom.: 28687 Cov.: 31

Gnomad AFR AF: 0.678

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.646

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.666

Gnomad SAS AF: 0.621

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.637

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

GnomAD4 genome AF: 0.610 AC: 92712 AN: 152026 Hom.: 28717 Cov.: 31 AF XY: 0.603 AC XY: 44818 AN XY: 74314

Gnomad4 AFR AF: 0.678

Gnomad4 AMR AF: 0.645

Gnomad4 ASJ AF: 0.624

Gnomad4 EAS AF: 0.666

Gnomad4 SAS AF: 0.620

Gnomad4 FIN AF: 0.451

Gnomad4 NFE AF: 0.578

Gnomad4 OTH AF: 0.638

Alfa AF: 0.583 Hom.: 3292

Bravo AF: 0.628

Asia WGS AF: 0.665 AC: 2315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	9.2
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6816285; hg19: chr4-102999609;