NM_014391.3:c.*569_*574dupTTTTTT

Variant names:

• chr10-90912291-T-TAAAAAA
• rs71025330
• NM_014391.3:c.*569_*574dupTTTTTT

Variant summary

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

The NM_014391.3(ANKRD1):​c.*569_*574dupTTTTTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.020 (106 hom., cov: 0)
  • Exomes 𝑓: 0.0085 (0 hom.)
• Consequence: ANKRD1 NM_014391.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

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 sas. gnomad4 allele frequency = 0.0199 (1398/70314) while in subpopulation SAS AF= 0.0242 (39/1612). AF 95% confidence interval is 0.0196. There are 106 homozygotes in gnomad4. There are 633 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 106 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD1	NM_014391.3	c.*569_*574dupTTTTTT		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.*569_*574dupTTTTTT		3_prime_UTR_variant	Exon 9 of 9	1	NM_014391.3	ENSP00000360762.3

Frequencies

GnomAD3 genomes AF: 0.0199 AC: 1399 AN: 70302 Hom.: 106 Cov.: 0

Gnomad AFR AF: 0.0180

Gnomad AMI AF: 0.00345

Gnomad AMR AF: 0.0149

Gnomad ASJ AF: 0.0368

Gnomad EAS AF: 0.0214

Gnomad SAS AF: 0.0241

Gnomad FIN AF: 0.0198

Gnomad MID AF: 0.0104

Gnomad NFE AF: 0.0208

Gnomad OTH AF: 0.0226

GnomAD4 exome AF: 0.00855 AC: 2 AN: 234 Hom.: 0 Cov.: 0 AF XY: 0.0189 AC XY: 2 AN XY: 106

Gnomad4 AMR exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.0125

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0199 AC: 1398 AN: 70314 Hom.: 106 Cov.: 0 AF XY: 0.0200 AC XY: 633 AN XY: 31582

Gnomad4 AFR AF: 0.0179

Gnomad4 AMR AF: 0.0149

Gnomad4 ASJ AF: 0.0368

Gnomad4 EAS AF: 0.0210

Gnomad4 SAS AF: 0.0242

Gnomad4 FIN AF: 0.0198

Gnomad4 NFE AF: 0.0208

Gnomad4 OTH AF: 0.0226

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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;