ENST00000655697.1:n.450+78101A>T

Variant names:

• chr2-149926216-A-T
• rs1437956
• ENST00000655697.1:n.450+78101A>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.450+78101A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 152,042 control chromosomes in the GnomAD database, including 8,774 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 0.34 (8774 hom., cov: 32)
• Consequence: MMADHC-DT ENST00000655697.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 2 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=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.409 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+78101A>T		intron_variant	Intron 3 of 3
MMADHC-DT	ENST00000657556.1	n.104-30277A>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50912 AN: 151926 Hom.: 8746 Cov.: 32

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.335 AC: 50987 AN: 152042 Hom.: 8774 Cov.: 32 AF XY: 0.341 AC XY: 25325 AN XY: 74290

African (AFR) AF: 0.375 AC: 15551 AN: 41454

American (AMR) AF: 0.387 AC: 5917 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.287 AC: 995 AN: 3468

East Asian (EAS) AF: 0.346 AC: 1782 AN: 5150

South Asian (SAS) AF: 0.425 AC: 2050 AN: 4828

European-Finnish (FIN) AF: 0.346 AC: 3646 AN: 10552

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.294 AC: 19979 AN: 67998

Other (OTH) AF: 0.349 AC: 738 AN: 2112

Alfa AF: 0.321 Hom.: 972

Bravo AF: 0.338

Asia WGS AF: 0.482 AC: 1675 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	0.24
DANN	Benign	0.41
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1437956; hg19: chr2-150782730;