4-101372387-C-T

Position:

• chr4-101372387-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 0.723 in 151,952 control chromosomes in the GnomAD database, including 40,271 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 0.72 (40271 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.809

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.101372387C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.723 AC: 109781 AN: 151834 Hom.: 40250 Cov.: 31

Gnomad AFR AF: 0.821

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.723

Gnomad EAS AF: 0.499

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.727

Gnomad OTH AF: 0.725

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

GnomAD4 genome AF: 0.723 AC: 109844 AN: 151952 Hom.: 40271 Cov.: 31 AF XY: 0.711 AC XY: 52803 AN XY: 74254

Gnomad4 AFR AF: 0.820

Gnomad4 AMR AF: 0.629

Gnomad4 ASJ AF: 0.723

Gnomad4 EAS AF: 0.500

Gnomad4 SAS AF: 0.590

Gnomad4 FIN AF: 0.628

Gnomad4 NFE AF: 0.727

Gnomad4 OTH AF: 0.718

Alfa AF: 0.717 Hom.: 17812

Bravo AF: 0.727

Asia WGS AF: 0.514 AC: 1789 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1822168; hg19: chr4-102293544;