rs7637878

Variant names:

• chr3-133475612-A-G
• rs7637878
• ENST00000833663.1:n.262+15290T>C

Variant summary

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

The ENST00000833663.1(BFSP2-AS1):​n.262+15290T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.774 in 152,078 control chromosomes in the GnomAD database, including 45,672 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 0.77 (45672 hom., cov: 31)
• Consequence: BFSP2-AS1 ENST00000833663.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.419
• Publications: 4 publications found

Genes affected

BFSP2-AS1 (HGNC:28425): (BFSP2 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.785 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BFSP2-AS1	NR_135276.2	n.208+15290T>C		intron_variant	Intron 1 of 5
BFSP2-AS1	NR_135277.2	n.208+15290T>C		intron_variant	Intron 1 of 3
BFSP2-AS1	NR_189055.1	n.208+15290T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BFSP2-AS1	ENST00000833663.1	n.262+15290T>C		intron_variant	Intron 1 of 1
BFSP2-AS1	ENST00000833664.1	n.256+15290T>C		intron_variant	Intron 1 of 2
BFSP2-AS1	ENST00000833665.1	n.214+15290T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.774 AC: 117620 AN: 151960 Hom.: 45625 Cov.: 31

Gnomad AFR AF: 0.792

Gnomad AMI AF: 0.807

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.833

Gnomad EAS AF: 0.705

Gnomad SAS AF: 0.801

Gnomad FIN AF: 0.726

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.785

Gnomad OTH AF: 0.782

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

GnomAD4 genome AF: 0.774 AC: 117722 AN: 152078 Hom.: 45672 Cov.: 31 AF XY: 0.769 AC XY: 57133 AN XY: 74324

African (AFR) AF: 0.792 AC: 32880 AN: 41490

American (AMR) AF: 0.704 AC: 10760 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.833 AC: 2891 AN: 3472

East Asian (EAS) AF: 0.705 AC: 3645 AN: 5170

South Asian (SAS) AF: 0.801 AC: 3861 AN: 4818

European-Finnish (FIN) AF: 0.726 AC: 7660 AN: 10546

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.785 AC: 53385 AN: 67986

Other (OTH) AF: 0.785 AC: 1658 AN: 2112

Alfa AF: 0.785 Hom.: 26711

Bravo AF: 0.773

Asia WGS AF: 0.754 AC: 2625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.66
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs7637878; hg19: chr3-133194456; COSMIC: COSV56587653;