rs7172582

chr15-67542218-T-C

Variant summary

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

The ENST00000604760.1(MAP2K5-DT):n.387A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.691 in 152,118 control chromosomes in the GnomAD database, including 37,071 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 (37065 hom., cov: 32)
  • Exomes 𝑓: 0.78 (6 hom.)
• Consequence: MAP2K5-DT ENST00000604760.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0120

Genes affected

MAP2K5-DT (HGNC:55261): (MAP2K5 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.773 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
MAP2K5-DT	ENST00000604760.1	n.387A>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.691 AC: 105077 AN: 151982 Hom.: 37049 Cov.: 32

Gnomad AFR AF: 0.553

Gnomad AMI AF: 0.785

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.778

Gnomad EAS AF: 0.582

Gnomad SAS AF: 0.712

Gnomad FIN AF: 0.653

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.778

Gnomad OTH AF: 0.710

GnomAD4 exome AF: 0.778 AC: 14 AN: 18 Hom.: 6 Cov.: 0 AF XY: 0.667 AC XY: 8 AN XY: 12

Gnomad4 FIN exome AF: 0.833

Gnomad4 NFE exome AF: 0.900

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.691 AC: 105133 AN: 152100 Hom.: 37065 Cov.: 32 AF XY: 0.683 AC XY: 50757 AN XY: 74352

Gnomad4 AFR AF: 0.553

Gnomad4 AMR AF: 0.705

Gnomad4 ASJ AF: 0.778

Gnomad4 EAS AF: 0.583

Gnomad4 SAS AF: 0.713

Gnomad4 FIN AF: 0.653

Gnomad4 NFE AF: 0.778

Gnomad4 OTH AF: 0.705

Alfa AF: 0.723 Hom.: 3757

Bravo AF: 0.690

Asia WGS AF: 0.644 AC: 2244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	7.0
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7172582; hg19: chr15-67834556;