chr15-67542218-T-C

Variant names:

• chr15-67542218-T-C
• rs7172582
• ENST00000604760.1:n.387A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_186334.1(MAP2K5-DT):​n.413A>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 NR_186334.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0120
• Publications: 8 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_186334.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAP2K5-DT	NR_186334.1		n.413A>G		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAP2K5-DT	ENST00000604760.1	TSL:6	n.387A>G		non_coding_transcript_exon	Exon 1 of 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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.833 AC: 5 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.900 AC: 9 AN: 10

Other (OTH) AF: 0.00 AC: 0 AN: 2

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

African (AFR) AF: 0.553 AC: 22942 AN: 41472

American (AMR) AF: 0.705 AC: 10782 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.778 AC: 2699 AN: 3470

East Asian (EAS) AF: 0.583 AC: 3012 AN: 5170

South Asian (SAS) AF: 0.713 AC: 3439 AN: 4822

European-Finnish (FIN) AF: 0.653 AC: 6906 AN: 10578

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.778 AC: 52913 AN: 67976

Other (OTH) AF: 0.705 AC: 1487 AN: 2110

Alfa AF: 0.718 Hom.: 5196

Bravo AF: 0.690

Asia WGS AF: 0.644 AC: 2244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.0
DANN	Benign	0.57
PhyloP100		0.012
PromoterAI		0.017	Neutral

Splicing

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

Other links and lift over

dbSNP: rs7172582; hg19: chr15-67834556;