10-97572621-TGGC-T

Position:

• chr10-97572621-TGGC-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The ENST00000307518.9(ANKRD2):​c.-86_-84del variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0235 in 1,472,248 control chromosomes in the GnomAD database, including 3,518 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.090 (1767 hom., cov: 32)
  • Exomes 𝑓: 0.016 (1751 hom.)
• Consequence: ANKRD2 ENST00000307518.9 5_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.44

Genes affected

ANKRD2 (HGNC:495): (ankyrin repeat domain 2) This gene encodes a protein that belongs to the muscle ankyrin repeat protein (MARP) family. A similar gene in rodents is a component of a muscle stress response pathway and plays a role in the stretch-response associated with slow muscle function. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Mar 2014]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 10-97572621-TGGC-T is Benign according to our data. Variant chr10-97572621-TGGC-T is described in ClinVar as [Benign]. Clinvar id is 776534.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANKRD2	NM_001291218.2	c.173_175del	p.Trp58_Pro59delinsSer	inframe_deletion	1/9		NP_001278147.1
ANKRD2	NM_001129981.3	c.-86_-84del		5_prime_UTR_variant	1/8		NP_001123453.1
ANKRD2	NM_020349.4	c.-86_-84del		5_prime_UTR_variant	1/9		NP_065082.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANKRD2	ENST00000298808.9	c.-86_-84del		5_prime_UTR_variant	1/8	1		ENSP00000298808
ANKRD2	ENST00000307518.9	c.-86_-84del		5_prime_UTR_variant	1/9	1		ENSP00000306163	P1

Frequencies

GnomAD3 genomes AF: 0.0896 AC: 13631 AN: 152098 Hom.: 1754 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0497

Gnomad ASJ AF: 0.0185

Gnomad EAS AF: 0.0793

Gnomad SAS AF: 0.0283

Gnomad FIN AF: 0.000659

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.00403

Gnomad OTH AF: 0.0718

GnomAD4 exome AF: 0.0158 AC: 20887 AN: 1320032 Hom.: 1751 AF XY: 0.0154 AC XY: 9896 AN XY: 643906

Gnomad4 AFR exome AF: 0.308

Gnomad4 AMR exome AF: 0.0634

Gnomad4 ASJ exome AF: 0.0205

Gnomad4 EAS exome AF: 0.0655

Gnomad4 SAS exome AF: 0.0247

Gnomad4 FIN exome AF: 0.000433

Gnomad4 NFE exome AF: 0.00319

Gnomad4 OTH exome AF: 0.0337

GnomAD4 genome AF: 0.0899 AC: 13677 AN: 152216 Hom.: 1767 Cov.: 32 AF XY: 0.0875 AC XY: 6512 AN XY: 74448

Gnomad4 AFR AF: 0.286

Gnomad4 AMR AF: 0.0496

Gnomad4 ASJ AF: 0.0185

Gnomad4 EAS AF: 0.0793

Gnomad4 SAS AF: 0.0286

Gnomad4 FIN AF: 0.000659

Gnomad4 NFE AF: 0.00403

Gnomad4 OTH AF: 0.0710

Alfa AF: 0.0541 Hom.: 120

Bravo AF: 0.105

Asia WGS AF: 0.0540 AC: 189 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 31, 2019

- -

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: rs17107819; hg19: chr10-99332378;