9-64411512-G-A

Position:

• chr9-64411512-G-A

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_Strong BP6_Moderate

The ENST00000357336.4(ANKRD20A5P):​n.2507G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0044 (0 hom., cov: 11)
  • Exomes 𝑓: 0.0037 (17 hom.)
  • Failed GnomAD Quality Control
• Consequence: ANKRD20A5P ENST00000357336.4 non_coding_transcript_exon
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.182

Genes affected

ANKRD20A5P (HGNC:):

ANKRD20A4P (HGNC:31982): (ankyrin repeat domain 20 family member A4, pseudogene)

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BP6: Variant 9-64411512-G-A is Benign according to our data. Variant chr9-64411512-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3239114.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANKRD20A4-ANKRD20A20P	NR_146419.1	n.2519G>A		non_coding_transcript_exon_variant	15/25

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANKRD20A5P	ENST00000357336.4	n.2507G>A		non_coding_transcript_exon_variant	15/15	1
ANKRD20A4P	ENST00000697282.1	n.2226G>A		non_coding_transcript_exon_variant	15/26

Frequencies

GnomAD3 genomes AF: 0.00 AC: 317 AN: 72464 Hom.: 0 Cov.: 11 FAILED QC

Gnomad AFR AF: 0.00285

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00702

Gnomad ASJ AF: 0.00881

Gnomad EAS AF: 0.00214

Gnomad SAS AF: 0.00834

Gnomad FIN AF: 0.00919

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00379

Gnomad OTH AF: 0.00407

GnomAD3 exomes AF: 0.000106 AC: 4 AN: 37732 Hom.: 0 AF XY: 0.0000530 AC XY: 1 AN XY: 18868

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00176

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000631

Gnomad OTH exome AF: 0.000756

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00373 AC: 4013 AN: 1077036 Hom.: 17 Cov.: 30 AF XY: 0.00396 AC XY: 2128 AN XY: 536976

Gnomad4 AFR exome AF: 0.00611

Gnomad4 AMR exome AF: 0.00367

Gnomad4 ASJ exome AF: 0.00778

Gnomad4 EAS exome AF: 0.00678

Gnomad4 SAS exome AF: 0.00288

Gnomad4 FIN exome AF: 0.0144

Gnomad4 NFE exome AF: 0.00299

Gnomad4 OTH exome AF: 0.00570

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00436 AC: 316 AN: 72452 Hom.: 0 Cov.: 11 AF XY: 0.00452 AC XY: 155 AN XY: 34326

Gnomad4 AFR AF: 0.00285

Gnomad4 AMR AF: 0.00687

Gnomad4 ASJ AF: 0.00881

Gnomad4 EAS AF: 0.00184

Gnomad4 SAS AF: 0.00904

Gnomad4 FIN AF: 0.00919

Gnomad4 NFE AF: 0.00379

Gnomad4 OTH AF: 0.00407

Alfa AF: 0.00561 Hom.: 2

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Sep 01, 2024

ANKRD20A4P: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.9
DANN	Benign	0.41

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: rs1431430514; hg19: chr9-69423930; COSMIC: COSV62005855;