ENST00000494869.2:n.632+12867G>T

Variant names:

• chr3-120380952-G-T
• rs11708297
• ENST00000494869.2:n.632+12867G>T

Variant summary

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

The ENST00000494869.2(BTNL12P):​n.632+12867G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.593 in 152,034 control chromosomes in the GnomAD database, including 27,476 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 0.59 (27476 hom., cov: 31)
• Consequence: BTNL12P ENST00000494869.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.816
• Publications: 5 publications found

Genes affected

BTNL12P (HGNC:):

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

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 = 0.781 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000494869.2. 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
	BTNL12P	NR_187254.1		n.996+12867G>T		intron	N/A
	BTNL12P	NR_187255.1		n.996+12867G>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BTNL12P	ENST00000494869.2	TSL:5	n.632+12867G>T		intron	N/A
	BTNL12P	ENST00000635496.2	TSL:5	n.180+12867G>T		intron	N/A
	BTNL12P	ENST00000732430.1		n.185+12867G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.593 AC: 90103 AN: 151916 Hom.: 27453 Cov.: 31

Gnomad AFR AF: 0.713

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.801

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.593 AC: 90172 AN: 152034 Hom.: 27476 Cov.: 31 AF XY: 0.592 AC XY: 44029 AN XY: 74320

African (AFR) AF: 0.713 AC: 29546 AN: 41466

American (AMR) AF: 0.417 AC: 6360 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1636 AN: 3470

East Asian (EAS) AF: 0.801 AC: 4141 AN: 5168

South Asian (SAS) AF: 0.667 AC: 3216 AN: 4824

European-Finnish (FIN) AF: 0.575 AC: 6076 AN: 10564

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.552 AC: 37494 AN: 67976

Other (OTH) AF: 0.545 AC: 1149 AN: 2108

Alfa AF: 0.546 Hom.: 38386

Bravo AF: 0.582

Asia WGS AF: 0.719 AC: 2503 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	2.4
DANN	Benign	0.92
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs11708297; hg19: chr3-120099799;