chr10-90912291-TAAA-T

Variant names:

• chr10-90912291-TAAA-T
• rs71025330
• NM_014391.3:c.*572_*574delTTT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The NM_014391.3(ANKRD1):​c.*572_*574delTTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0115 in 70,594 control chromosomes in the GnomAD database, including 11 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.012 (11 hom., cov: 0)
  • Exomes 𝑓: 0.017 (0 hom.)
• Consequence: ANKRD1 NM_014391.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.63

Genes affected

ANKRD1 (HGNC:15819): (ankyrin repeat domain 1) The protein encoded by this gene is localized to the nucleus of endothelial cells and is induced by IL-1 and TNF-alpha stimulation. Studies in rat cardiomyocytes suggest that this gene functions as a transcription factor. Interactions between this protein and the sarcomeric proteins myopalladin and titin suggest that it may also be involved in the myofibrillar stretch-sensor system. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0115 (810/70362) while in subpopulation AFR AF= 0.0343 (739/21554). AF 95% confidence interval is 0.0322. There are 11 homozygotes in gnomad4. There are 377 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 11 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD1	NM_014391.3	c.*572_*574delTTT		3_prime_UTR_variant	Exon 9 of 9	ENST00000371697.4	NP_055206.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKRD1	ENST00000371697	c.*572_*574delTTT		3_prime_UTR_variant	Exon 9 of 9	1	NM_014391.3	ENSP00000360762.3

Frequencies

GnomAD3 genomes AF: 0.0115 AC: 809 AN: 70348 Hom.: 11 Cov.: 0

Gnomad AFR AF: 0.0343

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00342

Gnomad ASJ AF: 0.00553

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00864

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000684

Gnomad OTH AF: 0.00452

GnomAD4 exome AF: 0.0172 AC: 4 AN: 232 Hom.: 0 AF XY: 0.0189 AC XY: 2 AN XY: 106

Gnomad4 AMR exome AF: 0.0200

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.0190

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0115 AC: 810 AN: 70362 Hom.: 11 Cov.: 0 AF XY: 0.0119 AC XY: 377 AN XY: 31614

Gnomad4 AFR AF: 0.0343

Gnomad4 AMR AF: 0.00342

Gnomad4 ASJ AF: 0.00553

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00866

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000684

Gnomad4 OTH AF: 0.00454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs71025330; hg19: chr10-92672048;