2-149707970-C-T

Position:

• chr2-149707970-C-T

Variant summary

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

The NR_110240.1(MMADHC-DT):​n.494-35748C>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 0.0859 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 NR_110240.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.314

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=-0.95).
• 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/exons	MANE	UniProt
MMADHC-DT	NR_110240.1	n.494-35748C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MMADHC-DT	ENST00000655697.1	n.202-35748C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0235

Gnomad4 AMR AF: 0.0575

Gnomad4 ASJ AF: 0.0787

Gnomad4 EAS AF: 0.0547

Gnomad4 SAS AF: 0.134

Gnomad4 FIN AF: 0.0913

Gnomad4 NFE AF: 0.127

Gnomad4 OTH AF: 0.0692

Alfa AF: 0.114 Hom.: 1383

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17801127; hg19: chr2-150564484;