chr10-90912291-TAAAAAA-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_014391.3(ANKRD1):​c.*569_*574delTTTTTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0641 in 234 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.063 (213 hom., cov: 0)
  • Exomes 𝑓: 0.064 (0 hom.)
  • Failed GnomAD Quality Control
• 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.

• BA1: GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0796 is higher than 0.05.

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes AF: 0.00 AC: 4458 AN: 70392 Hom.: 213 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0399

Gnomad ASJ AF: 0.0241

Gnomad EAS AF: 0.0770

Gnomad SAS AF: 0.0419

Gnomad FIN AF: 0.0871

Gnomad MID AF: 0.0313

Gnomad NFE AF: 0.0294

Gnomad OTH AF: 0.0566

GnomAD4 exome AF: 0.0641 AC: 15 AN: 234 Hom.: 0 AF XY: 0.0472 AC XY: 5 AN XY: 106

Gnomad4 AMR exome AF: 0.160

Gnomad4 EAS exome AF: 0.167

Gnomad4 SAS exome AF: 0.143

Gnomad4 NFE exome AF: 0.0250

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0633 AC: 4460 AN: 70404 Hom.: 213 Cov.: 0 AF XY: 0.0673 AC XY: 2129 AN XY: 31632

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.0398

Gnomad4 ASJ AF: 0.0241

Gnomad4 EAS AF: 0.0772

Gnomad4 SAS AF: 0.0420

Gnomad4 FIN AF: 0.0871

Gnomad4 NFE AF: 0.0294

Gnomad4 OTH AF: 0.0567

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;