6-26501930-G-T

Variant names:

• chr6-26501930-G-T
• NM_001732.3:c.420G>T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001732.3(BTN1A1):​c.420G>T​(p.Lys140Asn) variant causes a missense 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. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: BTN1A1 NM_001732.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.637

Genes affected

BTN1A1 (HGNC:1135): (butyrophilin subfamily 1 member A1) Butyrophilin is the major protein associated with fat droplets in the milk. It is a member of the immunoglobulin superfamily. It may have a cell surface receptor function. The human butyrophilin gene is localized in the major histocompatibility complex (MHC) class I region of 6p and may have arisen relatively recently in evolution by the shuffling of exons between 2 ancestral gene families [provided by RefSeq, Jul 2008]

ENSG00000291336 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.20883763).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BTN1A1	NM_001732.3	c.420G>T	p.Lys140Asn	missense_variant	Exon 3 of 8	ENST00000684113.1	NP_001723.2
LOC107986583	XR_001744057.3	n.5891-13786C>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BTN1A1	ENST00000684113.1	c.420G>T	p.Lys140Asn	missense_variant	Exon 3 of 8		NM_001732.3	ENSP00000507193.1
BTN1A1	ENST00000244513.10	c.420G>T	p.Lys140Asn	missense_variant	Exon 2 of 7	1		ENSP00000244513.6
ENSG00000291336	ENST00000707189.1	n.1000-51257G>T		intron_variant	Intron 1 of 1
ENSG00000291338	ENST00000707191.1	n.1001-30775G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Aug 30, 2021

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.420G>T (p.K140N) alteration is located in exon 2 (coding exon 2) of the BTN1A1 gene. This alteration results from a G to T substitution at nucleotide position 420, causing the lysine (K) at amino acid position 140 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.38
BayesDel_addAF	Benign	-0.29	T
BayesDel_noAF	Benign	-0.65
CADD	Benign	23
DANN	Uncertain	1.0
DEOGEN2	Benign	0.40	T;.
Eigen	Benign	0.025
Eigen_PC	Benign	-0.078
FATHMM_MKL	Benign	0.47	N
LIST_S2	Benign	0.27	T;T
M_CAP	Benign	0.0086	T
MetaRNN	Benign	0.21	T;T
MetaSVM	Benign	-0.94	T
MutationAssessor	Uncertain	2.3	M;.
PrimateAI	Benign	0.31	T
PROVEAN	Uncertain	-3.2	D;.
REVEL	Benign	0.097
Sift	Benign	0.032	D;.
Sift4G	Benign	0.071	T;T
Polyphen		0.97	D;.
Vest4		0.098
MutPred		0.60		Loss of ubiquitination at K140 (P = 0.0161);Loss of ubiquitination at K140 (P = 0.0161);
MVP		0.36
MPC		0.90
ClinPred		0.98	D
GERP RS		2.0
Varity_R		0.18
gMVP		0.44

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr6-26502158;