rs9400554

Variant names:

• chr6-95552246-C-T
• rs9400554
• ENST00000791249.1:n.266+7784G>A

Variant summary

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

The ENST00000791249.1(MANEA-DT):​n.266+7784G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.466 in 151,866 control chromosomes in the GnomAD database, including 16,606 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 0.47 (16606 hom., cov: 31)
• Consequence: MANEA-DT ENST00000791249.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0460
• Publications: 9 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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.527 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	ENST00000791249.1	n.266+7784G>A		intron_variant	Intron 3 of 3
MANEA-DT	ENST00000791250.1	n.440+14982G>A		intron_variant	Intron 2 of 2
MANEA-DT	ENST00000791251.1	n.559+7784G>A		intron_variant	Intron 3 of 3
MANEA-DT	ENST00000791252.1	n.87+14982G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.466 AC: 70763 AN: 151748 Hom.: 16596 Cov.: 31

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.466 AC: 70808 AN: 151866 Hom.: 16606 Cov.: 31 AF XY: 0.466 AC XY: 34557 AN XY: 74212

African (AFR) AF: 0.472 AC: 19535 AN: 41418

American (AMR) AF: 0.425 AC: 6488 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.528 AC: 1832 AN: 3468

East Asian (EAS) AF: 0.506 AC: 2603 AN: 5140

South Asian (SAS) AF: 0.545 AC: 2624 AN: 4818

European-Finnish (FIN) AF: 0.462 AC: 4864 AN: 10524

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.460 AC: 31248 AN: 67934

Other (OTH) AF: 0.493 AC: 1041 AN: 2110

Alfa AF: 0.465 Hom.: 27651

Bravo AF: 0.460

Asia WGS AF: 0.555 AC: 1931 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	1.0
DANN	Benign	0.61
PhyloP100		0.046

Splicing

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

Other links and lift over

dbSNP: rs9400554; hg19: chr6-96000122;