rs7637878

Positions:

• chr3-133475612-A-G

Variant summary

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

The NR_135277.1(BFSP2-AS1):​n.245+15290T>C variant causes a intron, non coding transcript 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 NR_135277.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.419

Genes affected

BFSP2-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
BFSP2-AS1	NR_135277.1	n.245+15290T>C		intron_variant, non_coding_transcript_variant
BFSP2-AS1	NR_135276.1	n.245+15290T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.792

Gnomad4 AMR AF: 0.704

Gnomad4 ASJ AF: 0.833

Gnomad4 EAS AF: 0.705

Gnomad4 SAS AF: 0.801

Gnomad4 FIN AF: 0.726

Gnomad4 NFE AF: 0.785

Gnomad4 OTH AF: 0.785

Alfa AF: 0.784 Hom.: 24308

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

Splicing

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

Publications

LitVar

Other links and lift over

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