rs1077014

Positions:

• chr8-2727451-T-A
• chr8-2727451-T-C

Variant summary

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

The ENST00000520024.1(ENSG00000253853):​n.134T>A 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 0.068 in 152,248 control chromosomes in the GnomAD database, including 475 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 0.068 (474 hom., cov: 32)
  • Exomes 𝑓: 0.17 (1 hom.)
• Consequence: ENSG00000253853 ENST00000520024.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.942

Genes affected

ENSG00000253853 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377785	NR_168441.1	n.496T>A		non_coding_transcript_exon_variant	1/12
LOC105377785	NR_168442.1	n.496T>A		non_coding_transcript_exon_variant	1/15
LOC105377785	NR_168443.1	n.496T>A		non_coding_transcript_exon_variant	1/9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000253853	ENST00000520024.1	n.134T>A		non_coding_transcript_exon_variant	1/5	3
ENSG00000253853	ENST00000654515.1	n.489T>A		non_coding_transcript_exon_variant	1/6
ENSG00000253853	ENST00000670600.1	n.496T>A		non_coding_transcript_exon_variant	1/2

Frequencies

GnomAD3 genomes AF: 0.0677 AC: 10294 AN: 152094 Hom.: 463 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0521

Gnomad ASJ AF: 0.0343

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.0796

Gnomad FIN AF: 0.0423

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0447

Gnomad OTH AF: 0.0630

GnomAD4 exome AF: 0.167 AC: 6 AN: 36 Hom.: 1 Cov.: 0 AF XY: 0.179 AC XY: 5 AN XY: 28

Gnomad4 AFR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.167

GnomAD4 genome AF: 0.0680 AC: 10353 AN: 152212 Hom.: 474 Cov.: 32 AF XY: 0.0682 AC XY: 5079 AN XY: 74424

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.0522

Gnomad4 ASJ AF: 0.0343

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.0800

Gnomad4 FIN AF: 0.0423

Gnomad4 NFE AF: 0.0447

Gnomad4 OTH AF: 0.0647

Alfa AF: 0.00888 Hom.: 0

Bravo AF: 0.0718

Asia WGS AF: 0.0980 AC: 343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.3
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1077014; hg19: chr8-2584991;