2-97245372-T-C

Variant names:

• chr2-97245372-T-C
• rs200455439
• NM_001354587.1:c.4707T>C

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.4707T>C​(p.Tyr1569Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00254 in 1,569,460 control chromosomes in the GnomAD database, including 60 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0022 (1 hom., cov: 19)
  • Exomes 𝑓: 0.0026 (59 hom.)
• Consequence: ANKRD36 NM_001354587.1 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.231

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=-0.9).
• BP6: Variant 2-97245372-T-C is Benign according to our data. Variant chr2-97245372-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 2651166.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=0.231 with no splicing effect.
• BS2: High Homozygotes in GnomAdExome4 at 59 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD36	NM_001354587.1	c.4707T>C	p.Tyr1569Tyr	synonymous_variant	Exon 71 of 76	ENST00000420699.9	NP_001341516.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKRD36	ENST00000420699.9	c.4707T>C	p.Tyr1569Tyr	synonymous_variant	Exon 71 of 76	5	NM_001354587.1	ENSP00000391950.4
ANKRD36	ENST00000461153.7	c.4707T>C	p.Tyr1569Tyr	synonymous_variant	Exon 71 of 75	5		ENSP00000419530.3
ANKRD36	ENST00000652721.1	c.4707T>C	p.Tyr1569Tyr	synonymous_variant	Exon 71 of 76			ENSP00000498611.1
ANKRD36	ENST00000421946.2	n.1927T>C		non_coding_transcript_exon_variant	Exon 13 of 14	2

Frequencies

GnomAD3 genomes AF: 0.00224 AC: 330 AN: 147510 Hom.: 1 Cov.: 19

Gnomad AFR AF: 0.000440

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00139

Gnomad ASJ AF: 0.000297

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00379

Gnomad FIN AF: 0.00711

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00290

Gnomad OTH AF: 0.00397

GnomAD3 exomes AF: 0.00243 AC: 390 AN: 160824 Hom.: 8 AF XY: 0.00261 AC XY: 222 AN XY: 85014

Gnomad AFR exome AF: 0.000772

Gnomad AMR exome AF: 0.000413

Gnomad ASJ exome AF: 0.000232

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00458

Gnomad FIN exome AF: 0.00546

Gnomad NFE exome AF: 0.00255

Gnomad OTH exome AF: 0.00312

GnomAD4 exome AF: 0.00257 AC: 3652 AN: 1421856 Hom.: 59 Cov.: 30 AF XY: 0.00279 AC XY: 1965 AN XY: 703944

Gnomad4 AFR exome AF: 0.000604

Gnomad4 AMR exome AF: 0.00114

Gnomad4 ASJ exome AF: 0.0000392

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00593

Gnomad4 FIN exome AF: 0.00573

Gnomad4 NFE exome AF: 0.00245

Gnomad4 OTH exome AF: 0.00217

GnomAD4 genome AF: 0.00224 AC: 330 AN: 147604 Hom.: 1 Cov.: 19 AF XY: 0.00257 AC XY: 184 AN XY: 71612

Gnomad4 AFR AF: 0.000439

Gnomad4 AMR AF: 0.00139

Gnomad4 ASJ AF: 0.000297

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00380

Gnomad4 FIN AF: 0.00711

Gnomad4 NFE AF: 0.00290

Gnomad4 OTH AF: 0.00395

Alfa AF: 0.00340 Hom.: 0

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jan 01, 2025

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	-0.90
CADD	Benign	1.3
DANN	Benign	0.23

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: rs200455439; hg19: chr2-97911109;