chr3-120371598-T-C

Variant names:

• chr3-120371598-T-C
• rs1606871
• ENST00000494869.2:n.632+3513T>C

Variant summary

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

The ENST00000494869.2(BTNL12P):​n.632+3513T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 151,960 control chromosomes in the GnomAD database, including 7,435 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 0.28 (7435 hom., cov: 32)
• Consequence: BTNL12P ENST00000494869.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.611
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.767 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+3513T>C		intron	N/A
	BTNL12P	NR_187255.1		n.996+3513T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BTNL12P	ENST00000494869.2	TSL:5	n.632+3513T>C		intron	N/A
	BTNL12P	ENST00000635496.2	TSL:5	n.180+3513T>C		intron	N/A
	BTNL12P	ENST00000732430.1		n.185+3513T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42202 AN: 151842 Hom.: 7435 Cov.: 32

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.787

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.178

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.278 AC: 42226 AN: 151960 Hom.: 7435 Cov.: 32 AF XY: 0.279 AC XY: 20716 AN XY: 74274

African (AFR) AF: 0.419 AC: 17351 AN: 41436

American (AMR) AF: 0.185 AC: 2827 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 593 AN: 3466

East Asian (EAS) AF: 0.787 AC: 4073 AN: 5174

South Asian (SAS) AF: 0.366 AC: 1765 AN: 4818

European-Finnish (FIN) AF: 0.196 AC: 2071 AN: 10574

Middle Eastern (MID) AF: 0.175 AC: 51 AN: 292

European-Non Finnish (NFE) AF: 0.188 AC: 12757 AN: 67920

Other (OTH) AF: 0.248 AC: 525 AN: 2116

Alfa AF: 0.201 Hom.: 5306

Bravo AF: 0.283

Asia WGS AF: 0.551 AC: 1909 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.4
DANN	Benign	0.74
PhyloP100		0.61

Splicing

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

Other links and lift over

dbSNP: rs1606871; hg19: chr3-120090445;