rs61741628

Variant names:

• chr19-34593562-G-A
• rs61741628
• NM_001025591.4:c.284C>T

Your query was ambiguous. Multiple possible variants found:

• chr19-34593562-G-A
• chr19-34593562-G-C
• chr19-34593562-G-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001025591.4(SCGB2B2):​c.284C>T​(p.Ala95Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000714 in 1,401,214 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A95D) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 7.1e-7 (0 hom.)
• Consequence: SCGB2B2 NM_001025591.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171

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)

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.11402771).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCGB2B2	NM_001025591.4	c.284C>T	p.Ala95Val	missense_variant	Exon 4 of 4	ENST00000601241.6	NP_001020762.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCGB2B2	ENST00000601241.6	c.284C>T	p.Ala95Val	missense_variant	Exon 4 of 4	2	NM_001025591.4	ENSP00000469876.1
SCGB2B2	ENST00000379204.2	c.284C>T	p.Ala95Val	missense_variant	Exon 3 of 3	1		ENSP00000368502.2
SCGB2B2	ENST00000595326.1	n.410C>T		non_coding_transcript_exon_variant	Exon 4 of 4	2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD3 exomes AF: 0.00000620 AC: 1 AN: 161418 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 84982

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.0000846

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 7.14e-7 AC: 1 AN: 1401214 Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0 AN XY: 691360

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000277

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.16
BayesDel_addAF	Benign	-0.46	T
BayesDel_noAF	Benign	-0.71
CADD	Benign	7.7
DANN	Benign	0.94
DEOGEN2	Benign	0.022	T;T
Eigen	Benign	-0.70
Eigen_PC	Benign	-0.97
FATHMM_MKL	Benign	0.0027	N
M_CAP	Benign	0.00058	T
MetaRNN	Benign	0.11	T;T
MetaSVM	Benign	-1.0	T
PrimateAI	Benign	0.47	T
PROVEAN	Uncertain	-3.0	D;.
REVEL	Benign	0.043
Polyphen		0.81	P;P
Vest4		0.058
MutPred		0.25		Gain of sheet (P = 0.0507);Gain of sheet (P = 0.0507);
MVP		0.030
MPC		0.044
ClinPred		0.27	T
GERP RS		0.046
Varity_R		0.32
gMVP		0.34

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: rs61741628; hg19: chr19-35084467;