NM_001025591.4:c.161C>A

Variant names:

• chr19-34594260-G-T
• NM_001025591.4:c.161C>A

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001025591.4(SCGB2B2):​c.161C>A​(p.Pro54His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: SCGB2B2 NM_001025591.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.171
• Publications: 0 publications found

Genes affected

SCGB2B2 (HGNC:27616): (secretoglobin family 2B member 2) Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

SCGB1B2P (HGNC:20741): (secretoglobin family 1B member 2, pseudogene)

ZNF807P (HGNC:33229): (zinc finger protein 807, pseudogene)

ENSG00000306401 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.20965356).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001025591.4. 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
	SCGB2B2	NM_001025591.4	MANE Select	c.161C>A	p.Pro54His	missense	Exon 3 of 4	NP_001020762.1	Q4G0G5
	SCGB2B2	NR_170947.1		n.1630C>A		non_coding_transcript_exon	Exon 2 of 3
	SCGB2B2	NR_170948.1		n.1630C>A		non_coding_transcript_exon	Exon 2 of 4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCGB2B2	ENST00000601241.6	TSL:2 MANE Select	c.161C>A	p.Pro54His	missense	Exon 3 of 4	ENSP00000469876.1	Q4G0G5
	SCGB2B2	ENST00000379204.2	TSL:1	c.161C>A	p.Pro54His	missense	Exon 2 of 3	ENSP00000368502.2	Q4G0G5
	SCGB2B2	ENST00000595326.1	TSL:2	n.373-661C>A		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.36
BayesDel_addAF	Benign	-0.27	T
BayesDel_noAF	Benign	-0.62
CADD	Benign	16
DANN	Benign	0.93
DEOGEN2	Benign	0.028	T
Eigen	Benign	-0.45
Eigen_PC	Benign	-0.76
FATHMM_MKL	Benign	0.0036	N
M_CAP	Benign	0.0024	T
MetaRNN	Benign	0.21	T
MetaSVM	Benign	-0.90	T
PhyloP100		0.17
PrimateAI	Uncertain	0.50	T
PROVEAN	Pathogenic	-9.0	D
REVEL	Benign	0.049
Sift4G	Pathogenic	0.0	D
Polyphen		1.0	D
Vest4		0.21
MutPred		0.13		Loss of glycosylation at P54 (P = 0.0375)
MVP		0.061
MPC		0.30
ClinPred		0.39	T
GERP RS		0.046
PromoterAI		0.10	Neutral
Varity_R		0.73
gMVP		0.26
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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

hg19: chr19-35085165;