rs17801127

Variant names:

• chr2-149707970-C-T
• rs17801127
• ENST00000449714.3:n.569-35748C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000449714.3(MMADHC-DT):​n.569-35748C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0859 in 152,128 control chromosomes in the GnomAD database, including 751 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 0.086 (751 hom., cov: 32)
• Consequence: MMADHC-DT ENST00000449714.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.314
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MMADHC-DT	NR_110240.1	n.494-35748C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MMADHC-DT	ENST00000449714.3	n.569-35748C>T		intron_variant	Intron 1 of 2	2
MMADHC-DT	ENST00000655697.1	n.202-35748C>T		intron_variant	Intron 1 of 3
MMADHC-DT	ENST00000687950.1	n.656-35748C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0860 AC: 13074 AN: 152010 Hom.: 752 Cov.: 32

Gnomad AFR AF: 0.0236

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.0577

Gnomad ASJ AF: 0.0787

Gnomad EAS AF: 0.0543

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.0913

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.0709

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

GnomAD4 genome AF: 0.0859 AC: 13067 AN: 152128 Hom.: 751 Cov.: 32 AF XY: 0.0841 AC XY: 6253 AN XY: 74372

African (AFR) AF: 0.0235 AC: 977 AN: 41526

American (AMR) AF: 0.0575 AC: 879 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0787 AC: 273 AN: 3468

East Asian (EAS) AF: 0.0547 AC: 283 AN: 5178

South Asian (SAS) AF: 0.134 AC: 645 AN: 4818

European-Finnish (FIN) AF: 0.0913 AC: 965 AN: 10564

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8639 AN: 67980

Other (OTH) AF: 0.0692 AC: 146 AN: 2110

Alfa AF: 0.111 Hom.: 1689

Bravo AF: 0.0782

Asia WGS AF: 0.0860 AC: 299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.93
DANN	Benign	0.41
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs17801127; hg19: chr2-150564484;