chr19-34591375-G-A

Variant names:

• chr19-34591375-G-A
• rs2169793
• NM_001025591.4:c.*2180C>T

Variant summary

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

The ENST00000601241.6(SCGB2B2):​c.*2180C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 152,096 control chromosomes in the GnomAD database, including 10,478 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 0.33 (10478 hom., cov: 32)
• Consequence: SCGB2B2 ENST00000601241.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.407
• Publications: 2 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)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000601241.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCGB2B2	NM_001025591.4	MANE Select	c.*2180C>T		3_prime_UTR	Exon 4 of 4	NP_001020762.1
	SCGB2B2	NR_170946.1		n.3755C>T		non_coding_transcript_exon	Exon 2 of 2
	SCGB2B2	NR_170947.1		n.3940C>T		non_coding_transcript_exon	Exon 3 of 3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCGB2B2	ENST00000601241.6	TSL:2 MANE Select	c.*2180C>T		3_prime_UTR	Exon 4 of 4	ENSP00000469876.1
	SCGB1B2P	ENST00000817528.1		n.289-13919C>T		intron	N/A
	SCGB1B2P	ENST00000817529.1		n.215-13643C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50672 AN: 151976 Hom.: 10489 Cov.: 32

Gnomad AFR AF: 0.0815

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.333 AC: 50651 AN: 152096 Hom.: 10478 Cov.: 32 AF XY: 0.336 AC XY: 24946 AN XY: 74340

African (AFR) AF: 0.0812 AC: 3373 AN: 41530

American (AMR) AF: 0.476 AC: 7278 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1562 AN: 3468

East Asian (EAS) AF: 0.464 AC: 2392 AN: 5158

South Asian (SAS) AF: 0.363 AC: 1749 AN: 4818

European-Finnish (FIN) AF: 0.420 AC: 4426 AN: 10550

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.421 AC: 28630 AN: 67954

Other (OTH) AF: 0.384 AC: 811 AN: 2112

Alfa AF: 0.394 Hom.: 6618

Bravo AF: 0.332

Asia WGS AF: 0.441 AC: 1532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.2
DANN	Benign	0.33
PhyloP100		0.41

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2169793; hg19: chr19-35082280;