2-150014346-C-T

Variant names:

• chr2-150014346-C-T
• rs331124
• ENST00000655697.1:n.451-29518C>T

Variant summary

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

The ENST00000655697.1(MMADHC-DT):​n.451-29518C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.897 in 151,982 control chromosomes in the GnomAD database, including 61,487 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 0.90 (61487 hom., cov: 32)
• Consequence: MMADHC-DT ENST00000655697.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.333

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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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.451-29518C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.897 AC: 136186 AN: 151864 Hom.: 61452 Cov.: 32

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.834

Gnomad AMR AF: 0.943

Gnomad ASJ AF: 0.969

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.965

Gnomad FIN AF: 0.927

Gnomad MID AF: 0.972

Gnomad NFE AF: 0.933

Gnomad OTH AF: 0.932

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

GnomAD4 genome AF: 0.897 AC: 136275 AN: 151982 Hom.: 61487 Cov.: 32 AF XY: 0.899 AC XY: 66743 AN XY: 74272

Gnomad4 AFR AF: 0.785

Gnomad4 AMR AF: 0.943

Gnomad4 ASJ AF: 0.969

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.965

Gnomad4 FIN AF: 0.927

Gnomad4 NFE AF: 0.933

Gnomad4 OTH AF: 0.932

Alfa AF: 0.932 Hom.: 87458

Bravo AF: 0.891

Asia WGS AF: 0.971 AC: 3375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.69
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs331124; hg19: chr2-150870860;