2-149993791-G-T

Position:

• chr2-149993791-G-T

Variant summary

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

The ENST00000655697.1(MMADHC-DT):​n.451-50073G>T 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 0.0701 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.487

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MMADHC-DT	ENST00000655697.1	n.451-50073G>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0953

Gnomad4 AMR AF: 0.0860

Gnomad4 ASJ AF: 0.0527

Gnomad4 EAS AF: 0.181

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.0620

Gnomad4 NFE AF: 0.0431

Gnomad4 OTH AF: 0.0696

Alfa AF: 0.0340 Hom.: 30

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10497042; hg19: chr2-150850305;