chr3-120387973-T-A

Variant names:

• chr3-120387973-T-A
• rs1733329
• ENST00000494869.2:n.632+19888T>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000494869.2(BTNL12P):​n.632+19888T>A variant causes a intron 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 30)
• Consequence: BTNL12P ENST00000494869.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 6 publications found

Genes affected

BTNL12P (HGNC:):

BTNL12P (HGNC:52935): (butyrophilin like 12, pseudogene)

PPDPFP1 (HGNC:56491): (PPDPF pseudogene 1)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BTNL12P	NR_187254.1	n.996+19888T>A		intron_variant	Intron 3 of 4
BTNL12P	NR_187255.1	n.996+19888T>A		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BTNL12P	ENST00000494869.2	n.632+19888T>A		intron_variant	Intron 3 of 4	5
BTNL12P	ENST00000635496.2	n.180+19888T>A		intron_variant	Intron 1 of 2	5
BTNL12P	ENST00000732430.1	n.185+19888T>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes Cov.: 30

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

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.10
DANN	Benign	0.68
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1733329; hg19: chr3-120106820;