2-97113752-A-T

Variant names:

• chr2-97113752-A-T
• rs774044606
• NM_001354587.1:c.13A>T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001354587.1(ANKRD36):​c.13A>T​(p.Lys5*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,457,752 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 31)
  • Exomes 𝑓: 0.0000027 (0 hom.)
• Consequence: ANKRD36 NM_001354587.1 stop_gained
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.52

Genes affected

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

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD36	NM_001354587.1	c.13A>T	p.Lys5*	stop_gained	Exon 1 of 76	ENST00000420699.9	NP_001341516.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKRD36	ENST00000420699.9	c.13A>T	p.Lys5*	stop_gained	Exon 1 of 76	5	NM_001354587.1	ENSP00000391950.4
ANKRD36	ENST00000452478.2	n.201A>T		non_coding_transcript_exon_variant	Exon 1 of 3	1
ANKRD36	ENST00000461153.7	c.13A>T	p.Lys5*	stop_gained	Exon 1 of 75	5		ENSP00000419530.3
ANKRD36	ENST00000652721.1	c.13A>T	p.Lys5*	stop_gained	Exon 1 of 76			ENSP00000498611.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD3 exomes AF: 0.00000935 AC: 2 AN: 213990 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 116420

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000217

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000274 AC: 4 AN: 1457752 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 725188

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000361

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 31

ExAC AF: 0.0000172 AC: 2

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.18	T
BayesDel_noAF	Benign	-0.50
CADD	Benign	18
DANN	Benign	0.90
Eigen	Benign	-0.65
Eigen_PC	Benign	-1.1
FATHMM_MKL	Benign	0.044	N
Vest4		0.074, 0.072, 0.066
GERP RS		-0.91
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs774044606; hg19: chr2-97779489;