2-97124550-G-A

Variant names:

• chr2-97124550-G-A
• rs141841093
• NM_001354587.1:c.684G>A

Variant summary

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

The NM_001354587.1(ANKRD36):​c.684G>A​(p.Ala228Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00289 in 1,553,120 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0018 (2 hom., cov: 30)
  • Exomes 𝑓: 0.0030 (10 hom.)
• Consequence: ANKRD36 NM_001354587.1 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.70

Genes affected

ANKRD36 (HGNC:24079): (ankyrin repeat domain 36)

ACMG classification

Verdict is Benign. Variant got -11 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BP6: Variant 2-97124550-G-A is Benign according to our data. Variant chr2-97124550-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2651159.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-2.7 with no splicing effect.
• BS2: High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD36	NM_001354587.1	c.684G>A	p.Ala228Ala	synonymous_variant	Exon 5 of 76	ENST00000420699.9	NP_001341516.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKRD36	ENST00000420699.9	c.684G>A	p.Ala228Ala	synonymous_variant	Exon 5 of 76	5	NM_001354587.1	ENSP00000391950.4
ANKRD36	ENST00000461153.7	c.684G>A	p.Ala228Ala	synonymous_variant	Exon 5 of 75	5		ENSP00000419530.3
ANKRD36	ENST00000652721.1	c.684G>A	p.Ala228Ala	synonymous_variant	Exon 5 of 76			ENSP00000498611.1

Frequencies

GnomAD3 genomes AF: 0.00186 AC: 282 AN: 151896 Hom.: 2 Cov.: 30

Gnomad AFR AF: 0.000435

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000724

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000209

Gnomad FIN AF: 0.00425

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00297

Gnomad OTH AF: 0.00239

GnomAD3 exomes AF: 0.00186 AC: 306 AN: 164162 Hom.: 2 AF XY: 0.00177 AC XY: 153 AN XY: 86296

Gnomad AFR exome AF: 0.000217

Gnomad AMR exome AF: 0.000845

Gnomad ASJ exome AF: 0.000115

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000218

Gnomad FIN exome AF: 0.00392

Gnomad NFE exome AF: 0.00303

Gnomad OTH exome AF: 0.00261

GnomAD4 exome AF: 0.00301 AC: 4212 AN: 1401108 Hom.: 10 Cov.: 30 AF XY: 0.00284 AC XY: 1961 AN XY: 691230

Gnomad4 AFR exome AF: 0.000314

Gnomad4 AMR exome AF: 0.00101

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000214

Gnomad4 FIN exome AF: 0.00440

Gnomad4 NFE exome AF: 0.00347

Gnomad4 OTH exome AF: 0.00311

GnomAD4 genome AF: 0.00185 AC: 281 AN: 152012 Hom.: 2 Cov.: 30 AF XY: 0.00167 AC XY: 124 AN XY: 74304

Gnomad4 AFR AF: 0.000434

Gnomad4 AMR AF: 0.000723

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000209

Gnomad4 FIN AF: 0.00425

Gnomad4 NFE AF: 0.00296

Gnomad4 OTH AF: 0.00237

Alfa AF: 0.00158 Hom.: 1

Bravo AF: 0.00174

Asia WGS AF: 0.000290 AC: 1 AN: 3462

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Mar 01, 2023

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

ANKRD36: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.6
DANN	Benign	0.22

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: rs141841093; hg19: chr2-97790287;