chr5-180947898-A-G

Position:

• chr5-180947898-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001040462.3(BTNL8):​c.787+273A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 1,221,076 control chromosomes in the GnomAD database, including 106,864 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 0.47 (17546 hom., cov: 32)
  • Exomes 𝑓: 0.41 (89318 hom.)
• Consequence: BTNL8 NM_001040462.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.645

Genes affected

BTNL8 (HGNC:26131): (butyrophilin like 8) Predicted to enable signaling receptor binding activity. Predicted to be involved in T cell receptor signaling pathway and regulation of cytokine production. Predicted to be located in plasma membrane. Predicted to be active in external side of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.626 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BTNL8	NM_001040462.3	c.787+273A>G		intron_variant		ENST00000340184.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BTNL8	ENST00000340184.9	c.787+273A>G		intron_variant		1	NM_001040462.3	P1

Frequencies

GnomAD3 genomes AF: 0.466 AC: 70842 AN: 152014 Hom.: 17508 Cov.: 32

Gnomad AFR AF: 0.632

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.434

GnomAD4 exome AF: 0.406 AC: 433650 AN: 1068944 Hom.: 89318 Cov.: 15 AF XY: 0.399 AC XY: 212849 AN XY: 533010

Gnomad4 AFR exome AF: 0.645

Gnomad4 AMR exome AF: 0.393

Gnomad4 ASJ exome AF: 0.247

Gnomad4 EAS exome AF: 0.359

Gnomad4 SAS exome AF: 0.256

Gnomad4 FIN exome AF: 0.418

Gnomad4 NFE exome AF: 0.416

Gnomad4 OTH exome AF: 0.400

GnomAD4 genome AF: 0.466 AC: 70933 AN: 152132 Hom.: 17546 Cov.: 32 AF XY: 0.462 AC XY: 34386 AN XY: 74366

Gnomad4 AFR AF: 0.633

Gnomad4 AMR AF: 0.438

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.346

Gnomad4 SAS AF: 0.264

Gnomad4 FIN AF: 0.427

Gnomad4 NFE AF: 0.415

Gnomad4 OTH AF: 0.430

Alfa AF: 0.456 Hom.: 2019

Bravo AF: 0.472

Asia WGS AF: 0.360 AC: 1250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.1
DANN	Benign	0.66

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: rs7711990; hg19: chr5-180374898; COSMIC: COSV51458998; COSMIC: COSV51458998;