rs1052369

Variant names:

• chr18-23599180-T-A
• rs1052369
• NM_173505.4:c.*2046A>T

Your query was ambiguous. Multiple possible variants found:

• chr18-23599180-T-A
• chr18-23599180-T-C
• chr18-23599180-T-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_173505.4. 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
	ANKRD29	NM_173505.4	MANE Select	c.*2046A>T		3_prime_UTR	Exon 10 of 10	NP_775776.2
	ANKRD29	NM_001308238.2		c.*2046A>T		3_prime_UTR	Exon 9 of 9	NP_001295167.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD29	ENST00000592179.6	TSL:1 MANE Select	c.*2046A>T		3_prime_UTR	Exon 10 of 10	ENSP00000468354.1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 1 AN: 2

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.862 AC: 35775 AN: 41522

American (AMR) AF: 0.606 AC: 9253 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1338 AN: 3470

East Asian (EAS) AF: 0.865 AC: 4478 AN: 5178

South Asian (SAS) AF: 0.687 AC: 3313 AN: 4820

European-Finnish (FIN) AF: 0.428 AC: 4524 AN: 10570

Middle Eastern (MID) AF: 0.462 AC: 135 AN: 292

European-Non Finnish (NFE) AF: 0.403 AC: 27369 AN: 67968

Other (OTH) AF: 0.520 AC: 1098 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.50
DANN	Benign	0.28
PhyloP100		-0.47
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1052369; hg19: chr18-21179144;