4-174900772-C-T

Position:

• chr4-174900772-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 0.77 in 152,030 control chromosomes in the GnomAD database, including 46,926 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 0.77 (46926 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.436

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.874 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.174900772C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADAM29	ENST00000507969.5	n.345-30214C>T		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.771 AC: 117083 AN: 151912 Hom.: 46922 Cov.: 31

Gnomad AFR AF: 0.526

Gnomad AMI AF: 0.913

Gnomad AMR AF: 0.816

Gnomad ASJ AF: 0.937

Gnomad EAS AF: 0.751

Gnomad SAS AF: 0.809

Gnomad FIN AF: 0.876

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.879

Gnomad OTH AF: 0.809

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

GnomAD4 genome AF: 0.770 AC: 117125 AN: 152030 Hom.: 46926 Cov.: 31 AF XY: 0.773 AC XY: 57464 AN XY: 74332

Gnomad4 AFR AF: 0.526

Gnomad4 AMR AF: 0.816

Gnomad4 ASJ AF: 0.937

Gnomad4 EAS AF: 0.750

Gnomad4 SAS AF: 0.810

Gnomad4 FIN AF: 0.876

Gnomad4 NFE AF: 0.880

Gnomad4 OTH AF: 0.808

Alfa AF: 0.836 Hom.: 10893

Bravo AF: 0.752

Asia WGS AF: 0.768 AC: 2674 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	0.23
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs985261; hg19: chr4-175821923;