chr6-95575879-A-T

Position:

• chr6-95575879-A-T

Variant summary

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

The ENST00000564541.1(MANEA-DT):​n.1572T>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 0.524 in 151,840 control chromosomes in the GnomAD database, including 21,267 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 0.52 (21266 hom., cov: 32)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: MANEA-DT ENST00000564541.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.153

Genes affected

MANEA-DT (HGNC:43732): (MANEA divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.778 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MANEA-DT	NR_104136.1	n.359+1214T>A		intron_variant, non_coding_transcript_variant
MANEA-DT	NR_047502.1	n.1573T>A		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MANEA-DT	ENST00000564541.1	n.1572T>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.524 AC: 79496 AN: 151720 Hom.: 21251 Cov.: 32

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.798

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.640

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.545

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

Gnomad4 FIN exome AF: 1.00

GnomAD4 genome AF: 0.524 AC: 79545 AN: 151838 Hom.: 21266 Cov.: 32 AF XY: 0.524 AC XY: 38858 AN XY: 74172

Gnomad4 AFR AF: 0.551

Gnomad4 AMR AF: 0.472

Gnomad4 ASJ AF: 0.533

Gnomad4 EAS AF: 0.798

Gnomad4 SAS AF: 0.668

Gnomad4 FIN AF: 0.471

Gnomad4 NFE AF: 0.495

Gnomad4 OTH AF: 0.548

Alfa AF: 0.499 Hom.: 2382

Bravo AF: 0.524

Asia WGS AF: 0.723 AC: 2510 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.7
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6937479; hg19: chr6-96023755;