rs1552472

chr17-30254002-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000386.4(BLMH):c.1217-4834C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0841 in 152,166 control chromosomes in the GnomAD database, including 832 homozygotes. 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: 𝑓 0.084 (832 hom., cov: 32)
• Consequence: BLMH NM_000386.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.20

Genes affected

BLMH (HGNC:1059): (bleomycin hydrolase) Bleomycin hydrolase (BMH) is a cytoplasmic cysteine peptidase that is highly conserved through evolution; however, the only known activity of the enzyme is metabolic inactivation of the glycopeptide bleomycin (BLM), an essential component of combination chemotherapy regimens for cancer. The protein contains the signature active site residues of the cysteine protease papain superfamily. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BLMH	NM_000386.4	c.1217-4834C>G		intron_variant		ENST00000261714.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BLMH	ENST00000261714.11	c.1217-4834C>G		intron_variant		1	NM_000386.4	P1
BLMH	ENST00000578090.5	c.*891-4834C>G		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0841 AC: 12785 AN: 152046 Hom.: 831 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0528

Gnomad ASJ AF: 0.0841

Gnomad EAS AF: 0.0454

Gnomad SAS AF: 0.0964

Gnomad FIN AF: 0.0442

Gnomad MID AF: 0.0828

Gnomad NFE AF: 0.0489

Gnomad OTH AF: 0.0829

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0841 AC: 12803 AN: 152166 Hom.: 832 Cov.: 32 AF XY: 0.0831 AC XY: 6179 AN XY: 74390

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.0526

Gnomad4 ASJ AF: 0.0841

Gnomad4 EAS AF: 0.0445

Gnomad4 SAS AF: 0.0959

Gnomad4 FIN AF: 0.0442

Gnomad4 NFE AF: 0.0489

Gnomad4 OTH AF: 0.0820

Alfa AF: 0.0700 Hom.: 62

Bravo AF: 0.0871

Asia WGS AF: 0.0800 AC: 277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
Cadd	Benign	14
Dann	Benign	0.89

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: rs1552472; hg19: chr17-28581020;