rs10170236

chr2-149601110-G-A

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+13260G>A 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 0.685 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 NR_110240.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.838 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MMADHC-DT	NR_110240.1	n.493+13260G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MMADHC-DT	ENST00000655697.1	n.201+13237G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.402

Gnomad4 AMR AF: 0.745

Gnomad4 ASJ AF: 0.803

Gnomad4 EAS AF: 0.859

Gnomad4 SAS AF: 0.769

Gnomad4 FIN AF: 0.850

Gnomad4 NFE AF: 0.792

Gnomad4 OTH AF: 0.705

Alfa AF: 0.745 Hom.: 10971

Bravo AF: 0.665

Asia WGS AF: 0.807 AC: 2802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.093
Dann	Benign	0.48
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

Publications

LitVar

Other links and lift over

dbSNP: rs10170236; hg19: chr2-150457624;