rs745720

Positions:

• chr2-150002026-C-T

Variant summary

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

The ENST00000655697.1(MMADHC-DT):​n.451-41838C>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 0.171 in 151,780 control chromosomes in the GnomAD database, including 2,384 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 0.17 (2384 hom., cov: 31)
• Consequence: MMADHC-DT ENST00000655697.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

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=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.251 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.451-41838C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.171 AC: 25910 AN: 151660 Hom.: 2372 Cov.: 31

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.171 AC: 25947 AN: 151780 Hom.: 2384 Cov.: 31 AF XY: 0.176 AC XY: 13051 AN XY: 74144

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.199

Gnomad4 SAS AF: 0.263

Gnomad4 FIN AF: 0.245

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.194

Alfa AF: 0.174 Hom.: 3718

Bravo AF: 0.165

Asia WGS AF: 0.309 AC: 1073 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.56
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs745720; hg19: chr2-150858540;