rs1437956

Positions:

• chr2-149926216-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+78101A>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 0.335 in 152,042 control chromosomes in the GnomAD database, including 8,774 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 0.34 (8774 hom., cov: 32)
• Consequence: MMADHC-DT ENST00000655697.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20

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=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MMADHC-DT	ENST00000655697.1	n.450+78101A>T		intron_variant, non_coding_transcript_variant
MMADHC-DT	ENST00000657556.1	n.104-30277A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50912 AN: 151926 Hom.: 8746 Cov.: 32

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.335 AC: 50987 AN: 152042 Hom.: 8774 Cov.: 32 AF XY: 0.341 AC XY: 25325 AN XY: 74290

Gnomad4 AFR AF: 0.375

Gnomad4 AMR AF: 0.387

Gnomad4 ASJ AF: 0.287

Gnomad4 EAS AF: 0.346

Gnomad4 SAS AF: 0.425

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.294

Gnomad4 OTH AF: 0.349

Alfa AF: 0.321 Hom.: 972

Bravo AF: 0.338

Asia WGS AF: 0.482 AC: 1675 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.24
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1437956; hg19: chr2-150782730;