chr2-149601110-G-A

Variant names:

• chr2-149601110-G-A
• rs10170236
• ENST00000449714.3:n.568+13237G>A

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+13237G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.685 in 152,072 control chromosomes in the GnomAD database, including 38,098 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 0.69 (38098 hom., cov: 33)
• Consequence: MMADHC-DT ENST00000449714.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42
• Publications: 12 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.838 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000449714.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MMADHC-DT	NR_110240.1		n.493+13260G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MMADHC-DT	ENST00000449714.3	TSL:2	n.568+13237G>A		intron	N/A
	MMADHC-DT	ENST00000655697.1		n.201+13237G>A		intron	N/A
	MMADHC-DT	ENST00000687950.1		n.655+13260G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.686 AC: 104177 AN: 151954 Hom.: 38082 Cov.: 33

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.745

Gnomad ASJ AF: 0.803

Gnomad EAS AF: 0.859

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.850

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.792

Gnomad OTH AF: 0.705

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

GnomAD4 genome AF: 0.685 AC: 104231 AN: 152072 Hom.: 38098 Cov.: 33 AF XY: 0.690 AC XY: 51280 AN XY: 74338

African (AFR) AF: 0.402 AC: 16664 AN: 41414

American (AMR) AF: 0.745 AC: 11379 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.803 AC: 2789 AN: 3472

East Asian (EAS) AF: 0.859 AC: 4443 AN: 5174

South Asian (SAS) AF: 0.769 AC: 3707 AN: 4820

European-Finnish (FIN) AF: 0.850 AC: 9010 AN: 10602

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.792 AC: 53848 AN: 68000

Other (OTH) AF: 0.705 AC: 1490 AN: 2112

Alfa AF: 0.682 Hom.: 25005

Bravo AF: 0.665

Asia WGS AF: 0.807 AC: 2802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.093
DANN	Benign	0.48
PhyloP100		-1.4
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

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

Other links and lift over

dbSNP: rs10170236; hg19: chr2-150457624;