rs2572386

chr8-11379466-A-G

Variant summary

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

The ENST00000481765.3(RN7SL293P):n.72A>G 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 0.478 in 152,120 control chromosomes in the GnomAD database, including 19,270 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 0.48 (19260 hom., cov: 32)
  • Exomes 𝑓: 0.46 (10 hom.)
• Consequence: RN7SL293P ENST00000481765.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

Genes affected

RN7SL293P (HGNC:46309): (RNA, 7SL, cytoplasmic 293, pseudogene)

FAM167A-AS1 (HGNC:15548): (FAM167A antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.675 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM167A-AS1	NR_026814.1	n.52-4347A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RN7SL293P	ENST00000481765.3	n.72A>G		non_coding_transcript_exon_variant	1/1
FAM167A-AS1	ENST00000533578.4	n.52-4347A>G		intron_variant, non_coding_transcript_variant		2
FAM167A-AS1	ENST00000655944.1	n.152+442A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72566 AN: 151924 Hom.: 19232 Cov.: 32

Gnomad AFR AF: 0.682

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.0185

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.472

GnomAD4 exome AF: 0.462 AC: 36 AN: 78 Hom.: 10 Cov.: 0 AF XY: 0.448 AC XY: 26 AN XY: 58

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 1.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.435

Gnomad4 OTH exome AF: 0.750

GnomAD4 genome AF: 0.478 AC: 72636 AN: 152042 Hom.: 19260 Cov.: 32 AF XY: 0.463 AC XY: 34388 AN XY: 74334

Gnomad4 AFR AF: 0.682

Gnomad4 AMR AF: 0.344

Gnomad4 ASJ AF: 0.558

Gnomad4 EAS AF: 0.0185

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.451

Gnomad4 OTH AF: 0.466

Alfa AF: 0.450 Hom.: 31706

Bravo AF: 0.484

Asia WGS AF: 0.198 AC: 693 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	4.1
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2572386; hg19: chr8-11236975;