rs950649

Positions:

• chr3-120365528-C-G

Variant summary

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

The XR_007096032.1(LOC124906274):​n.1082G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.762 in 151,806 control chromosomes in the GnomAD database, including 44,905 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 0.76 (44905 hom., cov: 29)
• Consequence: LOC124906274 XR_007096032.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.257

Genes affected

LOC124906274 (HGNC:):

BTNL12P (HGNC:52935): (butyrophilin like 12, pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124906274	XR_007096032.1	n.1082G>C		non_coding_transcript_exon_variant	3/3
LOC124906274	XR_007096033.1	n.1000G>C		non_coding_transcript_exon_variant	4/4
BTNL12P	NR_187254.1	n.316-932C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BTNL12P	ENST00000494869.2	n.14-994C>G		intron_variant		5
BTNL12P	ENST00000634410.2	n.173-923C>G		intron_variant		6
BTNL12P	ENST00000637360.1	n.281-932C>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.762 AC: 115513 AN: 151688 Hom.: 44843 Cov.: 29

Gnomad AFR AF: 0.929

Gnomad AMI AF: 0.632

Gnomad AMR AF: 0.685

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.813

Gnomad SAS AF: 0.794

Gnomad FIN AF: 0.694

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.723

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

GnomAD4 genome AF: 0.762 AC: 115634 AN: 151806 Hom.: 44905 Cov.: 29 AF XY: 0.761 AC XY: 56443 AN XY: 74140

Gnomad4 AFR AF: 0.929

Gnomad4 AMR AF: 0.685

Gnomad4 ASJ AF: 0.616

Gnomad4 EAS AF: 0.814

Gnomad4 SAS AF: 0.793

Gnomad4 FIN AF: 0.694

Gnomad4 NFE AF: 0.692

Gnomad4 OTH AF: 0.721

Alfa AF: 0.744 Hom.: 5294

Bravo AF: 0.766

Asia WGS AF: 0.818 AC: 2848 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.5
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs950649; hg19: chr3-120084375;