5-75611640-C-T

Variant names:

• chr5-75611640-C-T
• rs114367272
• NM_001276713.2:c.6C>T

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_001276713.2(ANKDD1B):​c.6C>T​(p.Asp2Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000371 in 1,079,324 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: 0.0000037 (0 hom.)
• Consequence: ANKDD1B NM_001276713.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.920
• Publications: 0 publications found

Genes affected

ANKDD1B (HGNC:32525): (ankyrin repeat and death domain containing 1B) Predicted to be involved in signal transduction. [provided by Alliance of Genome Resources, Apr 2022]

ANKDD1B Gene-Disease associations (from GenCC):

• ankylosing spondylitis

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BP7: Synonymous conserved (PhyloP=-0.92 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001276713.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKDD1B	NM_001276713.2	MANE Select	c.6C>T	p.Asp2Asp	synonymous	Exon 1 of 14	NP_001263642.1	A6NHY2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKDD1B	ENST00000601380.4	TSL:5 MANE Select	c.6C>T	p.Asp2Asp	synonymous	Exon 1 of 14	ENSP00000471417.1	A6NHY2
	ANKDD1B	ENST00000885189.1		c.6C>T	p.Asp2Asp	synonymous	Exon 1 of 14	ENSP00000555248.1
	ANKDD1B	ENST00000885191.1		c.6C>T	p.Asp2Asp	synonymous	Exon 1 of 12	ENSP00000555250.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 0.00000371 AC: 4 AN: 1079324 Hom.: 0 Cov.: 30 AF XY: 0.00000196 AC XY: 1 AN XY: 509634

African (AFR) AF: 0.00 AC: 0 AN: 22936

American (AMR) AF: 0.00 AC: 0 AN: 8402

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14364

East Asian (EAS) AF: 0.000151 AC: 4 AN: 26516

South Asian (SAS) AF: 0.00 AC: 0 AN: 19490

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 21108

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2914

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 919952

Other (OTH) AF: 0.00 AC: 0 AN: 43642

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.1
DANN	Benign	0.86
PhyloP100		-0.92
PromoterAI		0.056	Neutral

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

Other links and lift over

dbSNP: rs114367272; hg19: chr5-74907465;