rs745720

Variant names:

• chr2-150002026-C-T
• rs745720
• ENST00000655697.1:n.451-41838C>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.451-41838C>T variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 5 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=-0.8).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MMADHC-DT	ENST00000655697.1	n.451-41838C>T		intron_variant	Intron 3 of 3

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

African (AFR) AF: 0.119 AC: 4918 AN: 41380

American (AMR) AF: 0.222 AC: 3377 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 734 AN: 3470

East Asian (EAS) AF: 0.199 AC: 1021 AN: 5128

South Asian (SAS) AF: 0.263 AC: 1265 AN: 4814

European-Finnish (FIN) AF: 0.245 AC: 2573 AN: 10502

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11443 AN: 67946

Other (OTH) AF: 0.194 AC: 410 AN: 2110

Alfa AF: 0.171 Hom.: 8566

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
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs745720; hg19: chr2-150858540;