4-174900772-C-T

Variant names:

• chr4-174900772-C-T
• rs985261
• ENST00000507969.5:n.345-30214C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000507969.5(ADAM29):​n.345-30214C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ADAM29 ENST00000507969.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.436
• Publications: 2 publications found

Genes affected

ADAM29 (HGNC:207): (ADAM metallopeptidase domain 29) This gene encodes a member of the ADAM (a disintegrin and metalloprotease domain) family. Members of this family are membrane-anchored proteins structurally related to snake venom disintegrins, and have been implicated in a variety of biological processes involving cell-cell and cell-matrix interactions, including fertilization, muscle development, and neurogenesis. The protein encoded by this gene is highly expressed in testis and may be involved in human spermatogenesis. Alternative splicing results in multiple transcript variants that encode the same protein. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000507969.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADAM29	ENST00000507969.5	TSL:4	n.345-30214C>T		intron	N/A

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

African (AFR) AF: 0.526 AC: 21770 AN: 41410

American (AMR) AF: 0.816 AC: 12453 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.937 AC: 3251 AN: 3470

East Asian (EAS) AF: 0.750 AC: 3877 AN: 5168

South Asian (SAS) AF: 0.810 AC: 3906 AN: 4824

European-Finnish (FIN) AF: 0.876 AC: 9280 AN: 10590

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.880 AC: 59798 AN: 67988

Other (OTH) AF: 0.808 AC: 1704 AN: 2110

Alfa AF: 0.829 Hom.: 11015

Bravo AF: 0.752

Asia WGS AF: 0.768 AC: 2674 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.33
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs985261; hg19: chr4-175821923;