6-3150549-C-T

Position:

• chr6-3150549-C-T

Variant summary

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

The NM_004332.4(BPHL):​c.789-1939C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0302 in 152,302 control chromosomes in the GnomAD database, including 232 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 0.030 (232 hom., cov: 32)
• Consequence: BPHL NM_004332.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.26

Genes affected

BPHL (HGNC:1094): (biphenyl hydrolase like) This gene encodes a member of the serine protease family of hydrolytic enzymes which contain a serine in their active site. The encoded protein may play a role in activation of the antiviral prodrug valacyclovir. Alternatively spliced transcript variants have been described.[provided by RefSeq, Jan 2009]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BPHL	NM_004332.4	c.789-1939C>T		intron_variant		ENST00000380379.10
BPHL	NM_001302777.1	c.738-1939C>T		intron_variant
BPHL	NR_026648.2	n.1450-1939C>T		intron_variant, non_coding_transcript_variant
BPHL	NR_026649.2	n.1222-1939C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BPHL	ENST00000380379.10	c.789-1939C>T		intron_variant		1	NM_004332.4	P1
	ENST00000447644.1	n.544+1970G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0303 AC: 4604 AN: 152184 Hom.: 233 Cov.: 32

Gnomad AFR AF: 0.0288

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0139

Gnomad ASJ AF: 0.00375

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.0856

Gnomad FIN AF: 0.0439

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0120

Gnomad OTH AF: 0.0297

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

GnomAD4 genome AF: 0.0302 AC: 4605 AN: 152302 Hom.: 232 Cov.: 32 AF XY: 0.0336 AC XY: 2502 AN XY: 74464

Gnomad4 AFR AF: 0.0287

Gnomad4 AMR AF: 0.0139

Gnomad4 ASJ AF: 0.00375

Gnomad4 EAS AF: 0.274

Gnomad4 SAS AF: 0.0859

Gnomad4 FIN AF: 0.0439

Gnomad4 NFE AF: 0.0120

Gnomad4 OTH AF: 0.0327

Alfa AF: 0.0153 Hom.: 10

Bravo AF: 0.0280

Asia WGS AF: 0.164 AC: 568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.4
DANN	Benign	0.37

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: rs3799218; hg19: chr6-3150783;