4-147401777-T-C

Position:

• chr4-147401777-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 0.0759 in 152,236 control chromosomes in the GnomAD database, including 563 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 0.076 (563 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.216

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.106 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.147401777T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0760 AC: 11563 AN: 152118 Hom.: 565 Cov.: 32

Gnomad AFR AF: 0.0241

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.0883

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.000576

Gnomad SAS AF: 0.0591

Gnomad FIN AF: 0.0783

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.0951

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

GnomAD4 genome AF: 0.0759 AC: 11560 AN: 152236 Hom.: 563 Cov.: 32 AF XY: 0.0746 AC XY: 5556 AN XY: 74432

Gnomad4 AFR AF: 0.0241

Gnomad4 AMR AF: 0.0881

Gnomad4 ASJ AF: 0.122

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0595

Gnomad4 FIN AF: 0.0783

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.0937

Alfa AF: 0.0866 Hom.: 334

Bravo AF: 0.0756

Asia WGS AF: 0.0290 AC: 102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.1
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17023187; hg19: chr4-148322929;