2-149993791-G-T

Variant names:

• chr2-149993791-G-T
• rs10497042
• ENST00000655697.1:n.451-50073G>T

Variant summary

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

The ENST00000655697.1(MMADHC-DT):​n.451-50073G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0701 in 152,108 control chromosomes in the GnomAD database, including 477 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 0.070 (477 hom., cov: 32)
• Consequence: MMADHC-DT ENST00000655697.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.487
• Publications: 4 publications found

Genes affected

MMADHC-DT (HGNC:41087): (MMADHC divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.171 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
MMADHC-DT	ENST00000655697.1	n.451-50073G>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0701 AC: 10650 AN: 151990 Hom.: 475 Cov.: 32

Gnomad AFR AF: 0.0954

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0858

Gnomad ASJ AF: 0.0527

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0620

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0431

Gnomad OTH AF: 0.0699

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

GnomAD4 genome AF: 0.0701 AC: 10666 AN: 152108 Hom.: 477 Cov.: 32 AF XY: 0.0732 AC XY: 5442 AN XY: 74350

African (AFR) AF: 0.0953 AC: 3956 AN: 41496

American (AMR) AF: 0.0860 AC: 1313 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0527 AC: 183 AN: 3470

East Asian (EAS) AF: 0.181 AC: 930 AN: 5150

South Asian (SAS) AF: 0.103 AC: 496 AN: 4812

European-Finnish (FIN) AF: 0.0620 AC: 657 AN: 10594

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0431 AC: 2932 AN: 67992

Other (OTH) AF: 0.0696 AC: 147 AN: 2112

Alfa AF: 0.0364 Hom.: 36

Bravo AF: 0.0735

Asia WGS AF: 0.151 AC: 523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.66
DANN	Benign	0.53
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs10497042; hg19: chr2-150850305;