rs1437959

chr2-149917035-A-Gchr2-149917035-A-T

Variant summary

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

The ENST00000655697.1(MMADHC-DT):n.450+68920A>G 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 0.915 in 152,158 control chromosomes in the GnomAD database, including 63,826 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 0.91 (63826 hom., cov: 32)
• Consequence: MMADHC-DT ENST00000655697.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.678

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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MMADHC-DT	ENST00000655697.1	n.450+68920A>G		intron_variant, non_coding_transcript_variant
MMADHC-DT	ENST00000657556.1	n.104-39458A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.915 AC: 139086 AN: 152038 Hom.: 63770 Cov.: 32

Gnomad AFR AF: 0.853

Gnomad AMI AF: 0.834

Gnomad AMR AF: 0.949

Gnomad ASJ AF: 0.969

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.962

Gnomad FIN AF: 0.927

Gnomad MID AF: 0.978

Gnomad NFE AF: 0.930

Gnomad OTH AF: 0.942

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

GnomAD4 genome AF: 0.915 AC: 139198 AN: 152158 Hom.: 63826 Cov.: 32 AF XY: 0.916 AC XY: 68169 AN XY: 74388

Gnomad4 AFR AF: 0.853

Gnomad4 AMR AF: 0.949

Gnomad4 ASJ AF: 0.969

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.962

Gnomad4 FIN AF: 0.927

Gnomad4 NFE AF: 0.930

Gnomad4 OTH AF: 0.942

Alfa AF: 0.923 Hom.: 11439

Bravo AF: 0.913

Asia WGS AF: 0.975 AC: 3388 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	1.9
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1437959; hg19: chr2-150773549;