8-100957891-C-T

Position:

• chr8-100957891-C-T

Variant summary

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

The ENST00000476271.3(RN7SL685P):​n.9C>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 0.654 in 151,956 control chromosomes in the GnomAD database, including 33,082 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 0.65 (33074 hom., cov: 31)
  • Exomes 𝑓: 0.66 (8 hom.)
• Consequence: RN7SL685P ENST00000476271.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.534

Genes affected

RN7SL685P (HGNC:46701): (RNA, 7SL, cytoplasmic 685, pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.778 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RN7SL685P		n.100957891C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RN7SL685P	ENST00000476271.3	n.9C>T		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.654 AC: 99338 AN: 151806 Hom.: 33043 Cov.: 31

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.647

GnomAD4 exome AF: 0.656 AC: 21 AN: 32 Hom.: 8 Cov.: 0 AF XY: 0.607 AC XY: 17 AN XY: 28

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.750

Gnomad4 NFE exome AF: 0.650

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.654 AC: 99412 AN: 151924 Hom.: 33074 Cov.: 31 AF XY: 0.650 AC XY: 48266 AN XY: 74254

Gnomad4 AFR AF: 0.785

Gnomad4 AMR AF: 0.626

Gnomad4 ASJ AF: 0.624

Gnomad4 EAS AF: 0.609

Gnomad4 SAS AF: 0.699

Gnomad4 FIN AF: 0.516

Gnomad4 NFE AF: 0.606

Gnomad4 OTH AF: 0.640

Alfa AF: 0.639 Hom.: 4581

Bravo AF: 0.669

Asia WGS AF: 0.633 AC: 2205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.4
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4734500; hg19: chr8-101970119;