5-75611679-GGGGCTGCTGCTCC-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BS1 BS2

The NM_001276713.2(ANKDD1B):c.56_68del(p.Leu19ArgfsTer75) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0018 in 1,231,796 control chromosomes in the GnomAD database, including 34 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0086 (22 hom., cov: 31)
  • Exomes 𝑓: 0.00084 (12 hom.)
• Consequence: ANKDD1B NM_001276713.2 frameshift
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.11

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 5-75611679-GGGGCTGCTGCTCC-G is Benign according to our data. Variant chr5-75611679-GGGGCTGCTGCTCC-G is described in ClinVar as [Benign]. Clinvar id is 768006.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00859 (1308/152252) while in subpopulation AFR AF= 0.0301 (1252/41564). AF 95% confidence interval is 0.0287. There are 22 homozygotes in gnomad4. There are 624 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 22 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ANKDD1B	NM_001276713.2	c.56_68del	p.Leu19ArgfsTer75	frameshift_variant	1/14	ENST00000601380.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ANKDD1B	ENST00000601380.4	c.56_68del	p.Leu19ArgfsTer75	frameshift_variant	1/14	5	NM_001276713.2	P1

Frequencies

GnomAD3 genomes AF: 0.00855 AC: 1300 AN: 152134 Hom.: 22 Cov.: 31

Gnomad AFR AF: 0.0300

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00281

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000194

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0000441

Gnomad OTH AF: 0.00382

GnomAD3 exomes AF: 0.00376 AC: 1 AN: 266 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 158

Gnomad AFR exome AF: 0.125

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.000840 AC: 907 AN: 1079544 Hom.: 12 AF XY: 0.000738 AC XY: 376 AN XY: 509732

Gnomad4 AFR exome AF: 0.0327

Gnomad4 AMR exome AF: 0.00273

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.000226

Gnomad4 SAS exome AF: 0.0000513

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000348

Gnomad4 OTH exome AF: 0.00208

GnomAD4 genome AF: 0.00859 AC: 1308 AN: 152252 Hom.: 22 Cov.: 31 AF XY: 0.00838 AC XY: 624 AN XY: 74446

Gnomad4 AFR AF: 0.0301

Gnomad4 AMR AF: 0.00281

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000441

Gnomad4 OTH AF: 0.00378

Alfa AF: 0.00733 Hom.: 2

Bravo AF: 0.0101

Asia WGS AF: 0.00346 AC: 12 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs528097367; hg19: chr5-74907504;