chr2-39604090-C-A

Variant names:

• chr2-39604090-C-A
• rs1005427
• ENST00000415640.1:n.73-42172C>A

Variant summary

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

The ENST00000415640.1(MAP4K3-DT):​n.73-42172C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.875 in 152,200 control chromosomes in the GnomAD database, including 60,402 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 0.87 (60401 hom., cov: 32)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: MAP4K3-DT ENST00000415640.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.217

Genes affected

MAP4K3-DT (HGNC:54056): (MAP4K3 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 (NFE) allele frequency at 95% confidence interval = 0.981 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAP4K3-DT	ENST00000415640.1	n.73-42172C>A		intron_variant	Intron 1 of 2	3
MAP4K3-DT	ENST00000446698.6	n.530-20009C>A		intron_variant	Intron 5 of 5	5
MAP4K3-DT	ENST00000670934.1	n.522-25905C>A		intron_variant	Intron 5 of 5
MAP4K3-DT	ENST00000426083.5	n.*14C>A		downstream_gene_variant		1

Frequencies

GnomAD3 genomes AF: 0.875 AC: 133008 AN: 152080 Hom.: 60363 Cov.: 32

Gnomad AFR AF: 0.602

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.920

Gnomad ASJ AF: 0.991

Gnomad EAS AF: 0.957

Gnomad SAS AF: 0.986

Gnomad FIN AF: 0.999

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.987

Gnomad OTH AF: 0.903

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 FIN exome AF: 1.00

GnomAD4 genome AF: 0.875 AC: 133103 AN: 152198 Hom.: 60401 Cov.: 32 AF XY: 0.879 AC XY: 65405 AN XY: 74428

Gnomad4 AFR AF: 0.603

Gnomad4 AMR AF: 0.920

Gnomad4 ASJ AF: 0.991

Gnomad4 EAS AF: 0.957

Gnomad4 SAS AF: 0.987

Gnomad4 FIN AF: 0.999

Gnomad4 NFE AF: 0.987

Gnomad4 OTH AF: 0.902

Alfa AF: 0.917 Hom.: 5527

Bravo AF: 0.854

Asia WGS AF: 0.937 AC: 3256 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.16
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1005427; hg19: chr2-39831230;