chr6-26501683-C-G

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001732.3(BTN1A1):​c.173C>G​(p.Ala58Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Consequence

BTN1A1
NM_001732.3 missense

Scores

1
9
9

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 2.75

Publications

0 publications found
Variant links:
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]

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
BTN1A1NM_001732.3 linkc.173C>G p.Ala58Gly missense_variant Exon 3 of 8 ENST00000684113.1 NP_001723.2 Q13410Q4VAN2
LOC107986583XR_001744057.3 linkn.5891-13539G>C intron_variant Intron 1 of 3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
BTN1A1ENST00000684113.1 linkc.173C>G p.Ala58Gly missense_variant Exon 3 of 8 NM_001732.3 ENSP00000507193.1 Q13410

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
LINK: link

Submissions by phenotype

not specified Uncertain:1
Jan 08, 2025
Ambry Genetics
Significance:Uncertain significance
Review Status:criteria provided, single submitter
Collection Method:clinical testing

The c.173C>G (p.A58G) alteration is located in exon 2 (coding exon 2) of the BTN1A1 gene. This alteration results from a C to G substitution at nucleotide position 173, causing the alanine (A) at amino acid position 58 to be replaced by a glycine (G). 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
Benign
0.18
BayesDel_addAF
Benign
-0.15
T
BayesDel_noAF
Benign
-0.45
CADD
Uncertain
24
DANN
Uncertain
1.0
DEOGEN2
Uncertain
0.45
T;.
Eigen
Uncertain
0.49
Eigen_PC
Uncertain
0.37
FATHMM_MKL
Uncertain
0.80
D
LIST_S2
Benign
0.79
T;T
M_CAP
Benign
0.021
T
MetaRNN
Uncertain
0.48
T;T
MetaSVM
Benign
-1.2
T
MutationAssessor
Pathogenic
3.3
M;.
PhyloP100
2.7
PrimateAI
Benign
0.37
T
PROVEAN
Uncertain
-3.5
D;.
REVEL
Benign
0.17
Sift
Uncertain
0.0060
D;.
Sift4G
Uncertain
0.010
D;D
Polyphen
0.99
D;.
Vest4
0.42
MutPred
0.37
Gain of glycosylation at S57 (P = 0.0849);Gain of glycosylation at S57 (P = 0.0849);
MVP
0.62
MPC
1.1
ClinPred
0.98
D
GERP RS
5.9
PromoterAI
0.017
Neutral
Varity_R
0.37
gMVP
0.60
Mutation Taster
=80/20
polymorphism

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

Other links and lift over

hg19: chr6-26501911; API