rs16827293

Positions:

• chr2-149652818-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.493+64968C>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 0.149 in 152,028 control chromosomes in the GnomAD database, including 2,324 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 0.15 (2324 hom., cov: 32)
• Consequence: MMADHC-DT NR_110240.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.435

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.549 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MMADHC-DT	NR_110240.1	n.493+64968C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MMADHC-DT	ENST00000655697.1	n.201+64945C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22683 AN: 151910 Hom.: 2317 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.0928

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.149 AC: 22711 AN: 152028 Hom.: 2324 Cov.: 32 AF XY: 0.153 AC XY: 11382 AN XY: 74308

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.0928

Gnomad4 EAS AF: 0.566

Gnomad4 SAS AF: 0.278

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.140

Alfa AF: 0.135 Hom.: 637

Bravo AF: 0.147

Asia WGS AF: 0.407 AC: 1411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16827293; hg19: chr2-150509332;