6-3150549-C-T

Variant names:

• chr6-3150549-C-T
• rs3799218
• NM_004332.4:c.789-1939C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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]

ENSG00000228170 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004332.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BPHL	NM_004332.4	MANE Select	c.789-1939C>T		intron	N/A	NP_004323.2	Q86WA6-1
	BPHL	NM_001302777.1		c.738-1939C>T		intron	N/A	NP_001289706.1	Q49AI2
	BPHL	NR_026648.2		n.1450-1939C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BPHL	ENST00000380379.10	TSL:1 MANE Select	c.789-1939C>T		intron	N/A	ENSP00000369739.5	Q86WA6-1
	BPHL	ENST00000380375.4	TSL:1	c.738-1939C>T		intron	N/A	ENSP00000369734.3	Q86WA6-2
	BPHL	ENST00000424847.6	TSL:1	n.*882-1939C>T		intron	N/A	ENSP00000394072.2	F2Z2Q1

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

African (AFR) AF: 0.0287 AC: 1194 AN: 41572

American (AMR) AF: 0.0139 AC: 212 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.00375 AC: 13 AN: 3470

East Asian (EAS) AF: 0.274 AC: 1420 AN: 5186

South Asian (SAS) AF: 0.0859 AC: 415 AN: 4834

European-Finnish (FIN) AF: 0.0439 AC: 465 AN: 10596

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0120 AC: 814 AN: 68024

Other (OTH) AF: 0.0327 AC: 69 AN: 2110

Alfa AF: 0.0248 Hom.: 126

Bravo AF: 0.0280

Asia WGS AF: 0.164 AC: 568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.4
DANN	Benign	0.37
PhyloP100		1.3
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: rs3799218; hg19: chr6-3150783;