rs2587156

Positions:

• chr8-78810873-T-C

Variant summary

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

The ENST00000649603.1(MITA1):​n.403+5178T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.952 in 152,192 control chromosomes in the GnomAD database, including 69,093 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 0.95 (69093 hom., cov: 31)
• Consequence: MITA1 ENST00000649603.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

Genes affected

MITA1 (HGNC:56733): (metabolism induced tumor activator 1)

LOC105375914 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.979 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375914	XR_001745967.2	n.1224+5178T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MITA1	ENST00000649603.1	n.403+5178T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.952 AC: 144817 AN: 152074 Hom.: 69033 Cov.: 31

Gnomad AFR AF: 0.987

Gnomad AMI AF: 0.953

Gnomad AMR AF: 0.959

Gnomad ASJ AF: 0.978

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.978

Gnomad FIN AF: 0.917

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.928

Gnomad OTH AF: 0.954

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

GnomAD4 genome AF: 0.952 AC: 144936 AN: 152192 Hom.: 69093 Cov.: 31 AF XY: 0.952 AC XY: 70848 AN XY: 74400

Gnomad4 AFR AF: 0.987

Gnomad4 AMR AF: 0.959

Gnomad4 ASJ AF: 0.978

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.977

Gnomad4 FIN AF: 0.917

Gnomad4 NFE AF: 0.928

Gnomad4 OTH AF: 0.954

Alfa AF: 0.935 Hom.: 15819

Bravo AF: 0.957

Asia WGS AF: 0.987 AC: 3430 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2587156; hg19: chr8-79723108;