ENST00000655697.1:n.450+68920A>G

Variant names:

• chr2-149917035-A-G
• rs1437959
• ENST00000655697.1:n.450+68920A>G

Variant summary

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

The ENST00000655697.1(MMADHC-DT):​n.450+68920A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.915 in 152,158 control chromosomes in the GnomAD database, including 63,826 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 0.91 (63826 hom., cov: 32)
• Consequence: MMADHC-DT ENST00000655697.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.678

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=-0.97).
• 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.450+68920A>G		intron_variant	Intron 3 of 3
MMADHC-DT	ENST00000657556.1	n.104-39458A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.915 AC: 139086 AN: 152038 Hom.: 63770 Cov.: 32

Gnomad AFR AF: 0.853

Gnomad AMI AF: 0.834

Gnomad AMR AF: 0.949

Gnomad ASJ AF: 0.969

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.962

Gnomad FIN AF: 0.927

Gnomad MID AF: 0.978

Gnomad NFE AF: 0.930

Gnomad OTH AF: 0.942

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

GnomAD4 genome AF: 0.915 AC: 139198 AN: 152158 Hom.: 63826 Cov.: 32 AF XY: 0.916 AC XY: 68169 AN XY: 74388

Gnomad4 AFR AF: 0.853

Gnomad4 AMR AF: 0.949

Gnomad4 ASJ AF: 0.969

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.962

Gnomad4 FIN AF: 0.927

Gnomad4 NFE AF: 0.930

Gnomad4 OTH AF: 0.942

Alfa AF: 0.923 Hom.: 11439

Bravo AF: 0.913

Asia WGS AF: 0.975 AC: 3388 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.9
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1437959; hg19: chr2-150773549;