NM_197975.3:c.426C>T

Variant names:

• chr5-180997241-C-T
• rs77077795
• NM_197975.3:c.426C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_197975.3(BTNL3):​c.426C>T​(p.Ile142Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00389 in 1,464,426 control chromosomes in the GnomAD database, including 844 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.020 (362 hom., cov: 24)
  • Exomes 𝑓: 0.0022 (482 hom.)
• Consequence: BTNL3 NM_197975.3 synonymous
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.70
• Publications: 1 publications found

Genes affected

BTNL3 (HGNC:1143): (butyrophilin like 3) 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 integral component of membrane. Predicted to be active in external side of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000299843 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP6: Variant 5-180997241-C-T is Benign according to our data. Variant chr5-180997241-C-T is described in ClinVar as Benign. ClinVar VariationId is 781741.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0628 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_197975.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BTNL3	NM_197975.3	MANE Select	c.426C>T	p.Ile142Ile	synonymous	Exon 3 of 8	NP_932079.1	Q6UXE8-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BTNL3	ENST00000342868.7	TSL:1 MANE Select	c.426C>T	p.Ile142Ile	synonymous	Exon 3 of 8	ENSP00000341787.6	Q6UXE8-1
	BTNL3	ENST00000899564.1		c.426C>T	p.Ile142Ile	synonymous	Exon 3 of 8	ENSP00000569623.1
	BTNL3	ENST00000946317.1		c.78C>T	p.Ile26Ile	synonymous	Exon 2 of 7	ENSP00000616376.1

Frequencies

GnomAD3 genomes AF: 0.0201 AC: 2753 AN: 137238 Hom.: 362 Cov.: 24

Gnomad AFR AF: 0.0650

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00768

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000216

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0134

Gnomad NFE AF: 0.000434

Gnomad OTH AF: 0.0201

GnomAD2 exomes AF: 0.00515 AC: 1182 AN: 229476 AF XY: 0.00374

Gnomad AFR exome AF: 0.0665

Gnomad AMR exome AF: 0.00380

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000344

Gnomad OTH exome AF: 0.00255

GnomAD4 exome AF: 0.00221 AC: 2934 AN: 1327082 Hom.: 482 Cov.: 31 AF XY: 0.00185 AC XY: 1224 AN XY: 661710

African (AFR) AF: 0.0680 AC: 2238 AN: 32892

American (AMR) AF: 0.00450 AC: 182 AN: 40416

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25134

East Asian (EAS) AF: 0.00 AC: 0 AN: 36372

South Asian (SAS) AF: 0.000106 AC: 9 AN: 84686

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 47240

Middle Eastern (MID) AF: 0.00353 AC: 19 AN: 5388

European-Non Finnish (NFE) AF: 0.000223 AC: 223 AN: 999466

Other (OTH) AF: 0.00474 AC: 263 AN: 55488

GnomAD4 genome AF: 0.0201 AC: 2759 AN: 137344 Hom.: 362 Cov.: 24 AF XY: 0.0188 AC XY: 1257 AN XY: 66864

African (AFR) AF: 0.0649 AC: 2590 AN: 39886

American (AMR) AF: 0.00767 AC: 100 AN: 13040

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3342

East Asian (EAS) AF: 0.00 AC: 0 AN: 4636

South Asian (SAS) AF: 0.000216 AC: 1 AN: 4624

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8890

Middle Eastern (MID) AF: 0.0143 AC: 4 AN: 280

European-Non Finnish (NFE) AF: 0.000434 AC: 26 AN: 59950

Other (OTH) AF: 0.0199 AC: 38 AN: 1910

Alfa AF: 0.0123 Hom.: 26

Asia WGS AF: 0.00302 AC: 10 AN: 3324

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.42
DANN	Benign	0.54
PhyloP100		-2.7
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.26		Details are displayed if max score is > 0.2
DS_AL_spliceai		0.26		Position offset: -28

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

Other links and lift over

dbSNP: rs77077795; hg19: chr5-180424241; COSMIC: COSV104654624;