10-90912291-TAAAAAAAAAAAAAAAAA-TAAAAAAAAAAAA

Variant names:

• chr10-90912291-TAAAAA-T
• rs71025330
• NM_014391.3:c.*570_*574delTTTTT

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS1

The NM_014391.3(ANKRD1):​c.*570_*574delTTTTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0652 in 230 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 0.091 (214 hom., cov: 0)
  • Exomes 𝑓: 0.065 (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 Likely_benign. Variant got -4 ACMG points.

• BS1: Variant frequency is greater than expected in population amr. gnomad4_exome allele frequency = 0.0652 (15/230) while in subpopulation AMR AF= 0.0833 (4/48). AF 95% confidence interval is 0.0339. There are 0 homozygotes in gnomad4_exome. There are 3 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD1	NM_014391.3	c.*570_*574delTTTTT		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.*570_*574delTTTTT		3_prime_UTR_variant	Exon 9 of 9	1	NM_014391.3	ENSP00000360762.3

Frequencies

GnomAD3 genomes AF: 0.0908 AC: 6379 AN: 70252 Hom.: 213 Cov.: 0

Gnomad AFR AF: 0.0710

Gnomad AMI AF: 0.0381

Gnomad AMR AF: 0.0865

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.00209

Gnomad SAS AF: 0.0480

Gnomad FIN AF: 0.0524

Gnomad MID AF: 0.125

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.0803

GnomAD4 exome AF: 0.0652 AC: 15 AN: 230 Hom.: 0 AF XY: 0.0288 AC XY: 3 AN XY: 104

Gnomad4 AMR exome AF: 0.0833

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0833

Gnomad4 NFE exome AF: 0.0625

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0908 AC: 6380 AN: 70266 Hom.: 214 Cov.: 0 AF XY: 0.0881 AC XY: 2783 AN XY: 31598

Gnomad4 AFR AF: 0.0709

Gnomad4 AMR AF: 0.0869

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.00210

Gnomad4 SAS AF: 0.0475

Gnomad4 FIN AF: 0.0524

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.0805

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;