18-14752602-A-G

Position:

• chr18-14752602-A-G

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_Strong BP6_Moderate BP7 BS2

The NM_001367607.2(ANKRD30B):​c.258A>G​(p.Ala86Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00669 in 1,612,714 control chromosomes in the GnomAD database, including 52 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0056 (4 hom., cov: 33)
  • Exomes 𝑓: 0.0068 (48 hom.)
• Consequence: ANKRD30B NM_001367607.2 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.329

Genes affected

ANKRD30B (HGNC:24165): (ankyrin repeat domain 30B)

ANKRD30B (HGNC:):

ACMG classification

Verdict is Benign. Variant got -11 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BP6: Variant 18-14752602-A-G is Benign according to our data. Variant chr18-14752602-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2648607.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-0.329 with no splicing effect.
• BS2: High Homozygotes in GnomAd4 at 4 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANKRD30B	NM_001367607.2	c.258A>G	p.Ala86Ala	synonymous_variant	2/44	ENST00000690538.1	NP_001354536.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANKRD30B	ENST00000690538.1	c.258A>G	p.Ala86Ala	synonymous_variant	2/44		NM_001367607.2	ENSP00000510074.1

Frequencies

GnomAD3 genomes AF: 0.00564 AC: 858 AN: 152190 Hom.: 4 Cov.: 33

Gnomad AFR AF: 0.00133

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.00478

Gnomad ASJ AF: 0.0124

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000828

Gnomad FIN AF: 0.00602

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00886

Gnomad OTH AF: 0.00478

GnomAD3 exomes AF: 0.00506 AC: 1252 AN: 247242 Hom.: 6 AF XY: 0.00511 AC XY: 685 AN XY: 134072

Gnomad AFR exome AF: 0.00125

Gnomad AMR exome AF: 0.00254

Gnomad ASJ exome AF: 0.0108

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000594

Gnomad FIN exome AF: 0.00563

Gnomad NFE exome AF: 0.00775

Gnomad OTH exome AF: 0.00514

GnomAD4 exome AF: 0.00680 AC: 9938 AN: 1460406 Hom.: 48 Cov.: 31 AF XY: 0.00659 AC XY: 4790 AN XY: 726360

Gnomad4 AFR exome AF: 0.000927

Gnomad4 AMR exome AF: 0.00290

Gnomad4 ASJ exome AF: 0.0104

Gnomad4 EAS exome AF: 0.0000252

Gnomad4 SAS exome AF: 0.000430

Gnomad4 FIN exome AF: 0.00566

Gnomad4 NFE exome AF: 0.00793

Gnomad4 OTH exome AF: 0.00559

GnomAD4 genome AF: 0.00563 AC: 858 AN: 152308 Hom.: 4 Cov.: 33 AF XY: 0.00559 AC XY: 416 AN XY: 74480

Gnomad4 AFR AF: 0.00132

Gnomad4 AMR AF: 0.00477

Gnomad4 ASJ AF: 0.0124

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000829

Gnomad4 FIN AF: 0.00602

Gnomad4 NFE AF: 0.00887

Gnomad4 OTH AF: 0.00473

Alfa AF: 0.00629 Hom.: 2

Bravo AF: 0.00509

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

May 01, 2022

ANKRD30B: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.41
DANN	Benign	0.25

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: rs200428778; hg19: chr18-14752601; COSMIC: COSV62815284;