ENST00000481765.3:n.72A>G

Variant names:

• chr8-11379466-A-G
• rs2572386
• ENST00000481765.3:n.72A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 publications found

Genes affected

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

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
RN7SL293P		n.11379466A>G		intragenic_variant
FAM167A-AS1	NR_026814.1	n.52-4347A>G		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RN7SL293P	ENST00000481765.3	n.72A>G		non_coding_transcript_exon_variant	Exon 1 of 1	6
FAM167A-AS1	ENST00000533578.5	n.52-4347A>G		intron_variant	Intron 1 of 6	2
FAM167A-AS1	ENST00000655944.1	n.152+442A>G		intron_variant	Intron 1 of 2

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

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 4 AN: 4

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 2 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.435 AC: 27 AN: 62

Other (OTH) AF: 0.750 AC: 3 AN: 4

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

African (AFR) AF: 0.682 AC: 28262 AN: 41456

American (AMR) AF: 0.344 AC: 5255 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.558 AC: 1935 AN: 3470

East Asian (EAS) AF: 0.0185 AC: 96 AN: 5180

South Asian (SAS) AF: 0.281 AC: 1351 AN: 4808

European-Finnish (FIN) AF: 0.346 AC: 3656 AN: 10566

Middle Eastern (MID) AF: 0.521 AC: 152 AN: 292

European-Non Finnish (NFE) AF: 0.451 AC: 30675 AN: 67962

Other (OTH) AF: 0.466 AC: 984 AN: 2110

Alfa AF: 0.457 Hom.: 70135

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
PhyloP100		0.35
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs2572386; hg19: chr8-11236975;