rs9358946

Variant names:

• chr6-26478699-G-A
• rs9358946
• NR_038992.1:n.460C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_038992.1(LOC285819):​n.460C>T 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 0.17 in 152,042 control chromosomes in the GnomAD database, including 2,247 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 0.17 (2247 hom., cov: 32)
• Consequence: LOC285819 NR_038992.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.961
• Publications: 20 publications found

Genes affected

LOC285819 (HGNC:):

BTN1A1P1 (HGNC:51545): (butyrophilin subfamily 1 member A1 pseudogene 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC285819	NR_038992.1	n.460C>T		non_coding_transcript_exon_variant	Exon 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000291336	ENST00000707189.1	n.1000-74488G>A		intron_variant	Intron 1 of 1
ENSG00000291338	ENST00000707191.1	n.1001-54006G>A		intron_variant	Intron 1 of 1
ENSG00000300236	ENST00000770281.1	n.559-6506C>T		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25783 AN: 151924 Hom.: 2248 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.170 AC: 25796 AN: 152042 Hom.: 2247 Cov.: 32 AF XY: 0.164 AC XY: 12215 AN XY: 74308

African (AFR) AF: 0.204 AC: 8475 AN: 41452

American (AMR) AF: 0.111 AC: 1690 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 397 AN: 3468

East Asian (EAS) AF: 0.106 AC: 548 AN: 5172

South Asian (SAS) AF: 0.182 AC: 878 AN: 4826

European-Finnish (FIN) AF: 0.126 AC: 1327 AN: 10550

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.175 AC: 11903 AN: 67974

Other (OTH) AF: 0.152 AC: 320 AN: 2112

Alfa AF: 0.175 Hom.: 4187

Bravo AF: 0.169

Asia WGS AF: 0.145 AC: 505 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.3
DANN	Benign	0.54
PhyloP100		0.96

Splicing

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

Other links and lift over

dbSNP: rs9358946; hg19: chr6-26478927;