rs16827293

Variant names:

• chr2-149652818-C-T
• rs16827293
• ENST00000449714.3:n.568+64945C>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.568+64945C>T variant causes a intron 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 ENST00000449714.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.435
• Publications: 9 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=-0.87).
• 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 rank	MANE	Protein	UniProt
MMADHC-DT	NR_110240.1	n.493+64968C>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.568+64945C>T		intron_variant	Intron 1 of 2	2
MMADHC-DT	ENST00000655697.1	n.201+64945C>T		intron_variant	Intron 1 of 3
MMADHC-DT	ENST00000687950.1	n.655+64968C>T		intron_variant	Intron 1 of 2

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

African (AFR) AF: 0.115 AC: 4757 AN: 41474

American (AMR) AF: 0.134 AC: 2040 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0928 AC: 322 AN: 3468

East Asian (EAS) AF: 0.566 AC: 2909 AN: 5142

South Asian (SAS) AF: 0.278 AC: 1339 AN: 4816

European-Finnish (FIN) AF: 0.127 AC: 1344 AN: 10570

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9417 AN: 67980

Other (OTH) AF: 0.140 AC: 296 AN: 2112

Alfa AF: 0.145 Hom.: 3543

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
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs16827293; hg19: chr2-150509332;