3-15644301-CT-CTT

Variant names:

• chr3-15644301-C-CT
• rs397514361
• NM_001370658.1:c.400-8dupT

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP6

The ENST00000643237.3(BTD):​c.400-15_400-14insT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000347 in 1,610,248 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.0019 (0 hom., cov: 31)
  • Exomes 𝑓: 0.00018 (0 hom.)
• Consequence: BTD ENST00000643237.3 intron
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1 B:1
• Conservation: PhyloP100: -0.787
• Publications: 1 publications found

Genes affected

BTD (HGNC:1122): (biotinidase) The protein encoded by this gene functions to recycle protein-bound biotin by cleaving biocytin (biotin-epsilon-lysine), a normal product of carboxylase degradation, resulting in regeneration of free biotin. The encoded protein has also been shown to have biotinyl transferase activity. Mutations in this gene are associated with biotinidase deficiency. Multiple transcript variants encoding different isoforms have been described. [provided by RefSeq, Aug 2013]

BTD Gene-Disease associations (from GenCC):

• biotinidase deficiency

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Myriad Women’s Health, ClinGen, Orphanet, Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae)
• Leigh syndrome

  Inheritance: AR Classification: MODERATE Submitted by: ClinGen

ACMG classification

Our verdict: Likely_benign. The variant received -1 ACMG points.

• BP6: Variant 3-15644301-C-CT is Benign according to our data. Variant chr3-15644301-C-CT is described in ClinVar as Conflicting_classifications_of_pathogenicity. ClinVar VariationId is 25010.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000643237.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BTD	NM_001370658.1	MANE Select	c.400-8dupT		splice_region intron	N/A	NP_001357587.1
	BTD	NM_001281723.4		c.400-8dupT		splice_region intron	N/A	NP_001268652.2
	BTD	NM_001281724.3		c.400-8dupT		splice_region intron	N/A	NP_001268653.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BTD	ENST00000643237.3	MANE Select	c.400-15_400-14insT		intron	N/A	ENSP00000495254.2
	BTD	ENST00000303498.10	TSL:1	c.400-15_400-14insT		intron	N/A	ENSP00000306477.6
	BTD	ENST00000427382.2	TSL:4	c.400-15_400-14insT		intron	N/A	ENSP00000397113.2

Frequencies

GnomAD3 genomes AF: 0.00193 AC: 294 AN: 152010 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.00667

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000918

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000294

Gnomad OTH AF: 0.000956

GnomAD2 exomes AF: 0.000430 AC: 102 AN: 236966 AF XY: 0.000312

Gnomad AFR exome AF: 0.00585

Gnomad AMR exome AF: 0.000364

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00000948

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.000180 AC: 263 AN: 1458120 Hom.: 0 Cov.: 31 AF XY: 0.000156 AC XY: 113 AN XY: 725062

African (AFR) AF: 0.00625 AC: 209 AN: 33452

American (AMR) AF: 0.000295 AC: 13 AN: 44056

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26038

East Asian (EAS) AF: 0.00 AC: 0 AN: 39638

South Asian (SAS) AF: 0.0000583 AC: 5 AN: 85712

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53222

Middle Eastern (MID) AF: 0.000524 AC: 3 AN: 5726

European-Non Finnish (NFE) AF: 0.00000360 AC: 4 AN: 1109996

Other (OTH) AF: 0.000481 AC: 29 AN: 60280

GnomAD4 genome AF: 0.00195 AC: 296 AN: 152128 Hom.: 0 Cov.: 31 AF XY: 0.00179 AC XY: 133 AN XY: 74380

African (AFR) AF: 0.00669 AC: 278 AN: 41524

American (AMR) AF: 0.000916 AC: 14 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5176

South Asian (SAS) AF: 0.00 AC: 0 AN: 4804

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10588

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0000294 AC: 2 AN: 67966

Other (OTH) AF: 0.000946 AC: 2 AN: 2114

Alfa AF: 0.000507 Hom.: 0

Bravo AF: 0.00203

ClinVar

ClinVar submissions as Germline

Significance: Conflicting classifications of pathogenicity

Revision: criteria provided, conflicting classifications

Pathogenic	VUS	Benign	Condition
-	-	1	Biotinidase deficiency (1)
-	1	-	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.79
Mutation Taster		=100/0	polymorphism

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: rs397514361; hg19: chr3-15685808;