rs550176856

Variant names:

• chr2-97113864-A-C
• rs550176856
• NM_001354587.1:c.125A>C

Your query was ambiguous. Multiple possible variants found:

• chr2-97113864-A-C
• chr2-97113864-A-G
• chr2-97113864-A-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001354587.1(ANKRD36):​c.125A>C​(p.His42Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000137 in 1,460,006 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict 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: 32)
  • Exomes 𝑓: 0.000014 (0 hom.)
• Consequence: ANKRD36 NM_001354587.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.92

Genes affected

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

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.10056627).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD36	NM_001354587.1	c.125A>C	p.His42Pro	missense_variant	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.125A>C	p.His42Pro	missense_variant	Exon 1 of 76	5	NM_001354587.1	ENSP00000391950.4
ANKRD36	ENST00000452478.2	n.313A>C		non_coding_transcript_exon_variant	Exon 1 of 3	1
ANKRD36	ENST00000461153.7	c.125A>C	p.His42Pro	missense_variant	Exon 1 of 75	5		ENSP00000419530.3
ANKRD36	ENST00000652721.1	c.125A>C	p.His42Pro	missense_variant	Exon 1 of 76			ENSP00000498611.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD3 exomes AF: 0.00000804 AC: 2 AN: 248910 Hom.: 0 AF XY: 0.0000148 AC XY: 2 AN XY: 135202

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: 0.0000177

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000137 AC: 20 AN: 1460006 Hom.: 0 Cov.: 32 AF XY: 0.0000165 AC XY: 12 AN XY: 726354

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: 0.0000180

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ExAC AF: 0.00000827 AC: 1

EpiCase AF: 0.0000545

EpiControl AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.77
BayesDel_addAF	Benign	-0.23	T
BayesDel_noAF	Benign	-0.55
CADD	Benign	1.0
DANN	Benign	0.26
DEOGEN2	Benign	0.0036	.;.;.;T
Eigen	Benign	-1.4
Eigen_PC	Benign	-1.6
FATHMM_MKL	Benign	0.0036	N
LIST_S2	Benign	0.092	T;T;T;T
M_CAP	Benign	0.0049	T
MetaRNN	Benign	0.10	T;T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.6	.;.;.;L
PrimateAI	Uncertain	0.63	T
PROVEAN	Benign	0.17	.;N;.;N
REVEL	Benign	0.057
Sift	Benign	0.21	.;T;.;T
Sift4G	Benign	0.18	.;T;T;T
Polyphen		0.0040	.;.;.;B
Vest4		0.17, 0.21, 0.13
MutPred		0.51		Loss of MoRF binding (P = 0.0577);Loss of MoRF binding (P = 0.0577);Loss of MoRF binding (P = 0.0577);Loss of MoRF binding (P = 0.0577);
MVP		0.46
ClinPred		0.085	T
GERP RS		-1.9
Varity_R		0.037

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: rs550176856; hg19: chr2-97779601;