6-95527519-C-T

Variant names:

• chr6-95527519-C-T
• rs2380222
• ENST00000791250.1:n.*177G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000791250.1(MANEA-DT):​n.*177G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.846 in 151,860 control chromosomes in the GnomAD database, including 54,711 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 0.85 (54711 hom., cov: 32)
• Consequence: MANEA-DT ENST00000791250.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.153
• Publications: 6 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.919 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MANEA-DT	ENST00000791250.1	n.*177G>A		downstream_gene_variant
MANEA-DT	ENST00000791252.1	n.*177G>A		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.846 AC: 128330 AN: 151742 Hom.: 54663 Cov.: 32

Gnomad AFR AF: 0.927

Gnomad AMI AF: 0.895

Gnomad AMR AF: 0.698

Gnomad ASJ AF: 0.823

Gnomad EAS AF: 0.916

Gnomad SAS AF: 0.827

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.837

Gnomad OTH AF: 0.834

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.846 AC: 128435 AN: 151860 Hom.: 54711 Cov.: 32 AF XY: 0.840 AC XY: 62311 AN XY: 74196

African (AFR) AF: 0.927 AC: 38507 AN: 41530

American (AMR) AF: 0.697 AC: 10610 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.823 AC: 2851 AN: 3466

East Asian (EAS) AF: 0.915 AC: 4731 AN: 5168

South Asian (SAS) AF: 0.827 AC: 3980 AN: 4812

European-Finnish (FIN) AF: 0.778 AC: 8221 AN: 10572

Middle Eastern (MID) AF: 0.844 AC: 248 AN: 294

European-Non Finnish (NFE) AF: 0.837 AC: 56711 AN: 67784

Other (OTH) AF: 0.836 AC: 1760 AN: 2106

Alfa AF: 0.832 Hom.: 30104

Bravo AF: 0.843

Asia WGS AF: 0.866 AC: 2983 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	4.9
DANN	Benign	0.72
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs2380222; hg19: chr6-95975395;