chr18-23599180-T-A

Position:

• chr18-23599180-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_173505.4(ANKRD29):​c.*2046A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.576 in 152,116 control chromosomes in the GnomAD database, including 28,578 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 0.58 (28578 hom., cov: 32)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: ANKRD29 NM_173505.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.471

Genes affected

ANKRD29 (HGNC:27110): (ankyrin repeat domain 29) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.854 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANKRD29	NM_173505.4	c.*2046A>T		3_prime_UTR_variant	10/10	ENST00000592179.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKRD29	ENST00000592179.6	c.*2046A>T		3_prime_UTR_variant	10/10	1	NM_173505.4	P1

Frequencies

GnomAD3 genomes AF: 0.576 AC: 87556 AN: 151996 Hom.: 28528 Cov.: 32

Gnomad AFR AF: 0.861

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.866

Gnomad SAS AF: 0.687

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.518

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.576 AC: 87670 AN: 152114 Hom.: 28578 Cov.: 32 AF XY: 0.581 AC XY: 43208 AN XY: 74338

Gnomad4 AFR AF: 0.862

Gnomad4 AMR AF: 0.606

Gnomad4 ASJ AF: 0.386

Gnomad4 EAS AF: 0.865

Gnomad4 SAS AF: 0.687

Gnomad4 FIN AF: 0.428

Gnomad4 NFE AF: 0.403

Gnomad4 OTH AF: 0.520

Alfa AF: 0.483 Hom.: 2647

Bravo AF: 0.601

Asia WGS AF: 0.763 AC: 2649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.50
DANN	Benign	0.28

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1052369; hg19: chr18-21179144;