17-30271699-G-T

Variant names:

• chr17-30271699-G-T
• rs3816828
• NM_000386.4:c.1029-311C>A

Variant summary

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

The NM_000386.4(BLMH):​c.1029-311C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.532 in 152,082 control chromosomes in the GnomAD database, including 23,477 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 0.53 (23477 hom., cov: 32)
• Consequence: BLMH NM_000386.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.136
• Publications: 3 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]

ENSG00000266120 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BLMH	NM_000386.4	c.1029-311C>A		intron_variant	Intron 9 of 11	ENST00000261714.11	NP_000377.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BLMH	ENST00000261714.11	c.1029-311C>A		intron_variant	Intron 9 of 11	1	NM_000386.4	ENSP00000261714.6

Frequencies

GnomAD3 genomes AF: 0.531 AC: 80761 AN: 151964 Hom.: 23417 Cov.: 32

Gnomad AFR AF: 0.771

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.532 AC: 80886 AN: 152082 Hom.: 23477 Cov.: 32 AF XY: 0.527 AC XY: 39206 AN XY: 74330

African (AFR) AF: 0.771 AC: 31993 AN: 41490

American (AMR) AF: 0.467 AC: 7143 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1352 AN: 3464

East Asian (EAS) AF: 0.215 AC: 1112 AN: 5174

South Asian (SAS) AF: 0.395 AC: 1903 AN: 4818

European-Finnish (FIN) AF: 0.493 AC: 5197 AN: 10552

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.449 AC: 30554 AN: 67986

Other (OTH) AF: 0.490 AC: 1035 AN: 2112

Alfa AF: 0.391 Hom.: 1385

Bravo AF: 0.536

Asia WGS AF: 0.402 AC: 1396 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.1
DANN	Benign	0.38
PhyloP100		0.14
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: rs3816828; hg19: chr17-28598717;