8-78907881-A-G

Variant names:

• chr8-78907881-A-G
• rs7836241
• ENST00000649603.1:n.404-25862A>G

Variant summary

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

The ENST00000649603.1(ENSG00000285744):​n.404-25862A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.576 in 151,894 control chromosomes in the GnomAD database, including 26,619 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 0.58 (26619 hom., cov: 32)
• Consequence: ENSG00000285744 ENST00000649603.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.169

Genes affected

ENSG00000285744 (HGNC:56733): (metabolism induced tumor activator 1)

LOC105375912 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MITA1	XR_001745965.2	n.1225-25862A>G		intron_variant	Intron 1 of 2
MITA1	XR_001745967.2	n.3285-25862A>G		intron_variant	Intron 2 of 3
MITA1	XR_001745970.2	n.1225-1127A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285744	ENST00000649603.1	n.404-25862A>G		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.575 AC: 87308 AN: 151778 Hom.: 26570 Cov.: 32

Gnomad AFR AF: 0.772

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.775

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.576 AC: 87417 AN: 151894 Hom.: 26619 Cov.: 32 AF XY: 0.571 AC XY: 42385 AN XY: 74212

Gnomad4 AFR AF: 0.772

Gnomad4 AMR AF: 0.536

Gnomad4 ASJ AF: 0.584

Gnomad4 EAS AF: 0.774

Gnomad4 SAS AF: 0.445

Gnomad4 FIN AF: 0.438

Gnomad4 NFE AF: 0.479

Gnomad4 OTH AF: 0.593

Alfa AF: 0.471 Hom.: 8620

Bravo AF: 0.595

Asia WGS AF: 0.658 AC: 2288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.56
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7836241; hg19: chr8-79820116;