chr17-30284376-G-A

Variant names:

• chr17-30284376-G-A
• rs7214014
• NM_000386.4:c.645+1012C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000386.4(BLMH):​c.645+1012C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.536 in 152,014 control chromosomes in the GnomAD database, including 23,938 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 0.54 (23938 hom., cov: 31)
• Consequence: BLMH NM_000386.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.220
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.779 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000386.4. 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
	BLMH	NM_000386.4	MANE Select	c.645+1012C>T		intron	N/A	NP_000377.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BLMH	ENST00000261714.11	TSL:1 MANE Select	c.645+1012C>T		intron	N/A	ENSP00000261714.6
	BLMH	ENST00000584603.2	TSL:5	c.645+1012C>T		intron	N/A	ENSP00000468486.1
	BLMH	ENST00000581037.5	TSL:5	c.291+1012C>T		intron	N/A	ENSP00000462442.1

Frequencies

GnomAD3 genomes AF: 0.535 AC: 81327 AN: 151896 Hom.: 23874 Cov.: 31

Gnomad AFR AF: 0.786

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.536 AC: 81456 AN: 152014 Hom.: 23938 Cov.: 31 AF XY: 0.531 AC XY: 39455 AN XY: 74306

African (AFR) AF: 0.786 AC: 32599 AN: 41456

American (AMR) AF: 0.468 AC: 7146 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.391 AC: 1357 AN: 3470

East Asian (EAS) AF: 0.215 AC: 1111 AN: 5174

South Asian (SAS) AF: 0.394 AC: 1902 AN: 4822

European-Finnish (FIN) AF: 0.493 AC: 5196 AN: 10530

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.449 AC: 30507 AN: 67972

Other (OTH) AF: 0.492 AC: 1040 AN: 2112

Alfa AF: 0.473 Hom.: 9568

Bravo AF: 0.541

Asia WGS AF: 0.403 AC: 1401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.0
DANN	Benign	0.39
PhyloP100		0.22
Mutation Taster		=100/0	polymorphism (auto)

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: rs7214014; hg19: chr17-28611394;