chr4-176995720-T-G

Position:

• chr4-176995720-T-G

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 0.0886 in 152,220 control chromosomes in the GnomAD database, including 825 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 0.089 (825 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0600

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 (NFE) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.176995720T>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000287544	ENST00000656694.1	n.347-101815A>C		intron_variant
ENSG00000287544	ENST00000662794.1	n.420-15629A>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0886 AC: 13483 AN: 152102 Hom.: 824 Cov.: 31

Gnomad AFR AF: 0.0240

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.0637

Gnomad ASJ AF: 0.0908

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0704

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.0922

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

GnomAD4 genome AF: 0.0886 AC: 13482 AN: 152220 Hom.: 825 Cov.: 31 AF XY: 0.0853 AC XY: 6348 AN XY: 74416

Gnomad4 AFR AF: 0.0239

Gnomad4 AMR AF: 0.0636

Gnomad4 ASJ AF: 0.0908

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.100

Gnomad4 FIN AF: 0.0704

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.0917

Alfa AF: 0.118 Hom.: 1525

Bravo AF: 0.0849

Asia WGS AF: 0.0850 AC: 297 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	1.8
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13110230; hg19: chr4-177916874;