rs2058619

Variant names:

• chr2-39627308-A-C
• rs2058619
• ENST00000415640.1:n.73-18954A>C

Variant summary

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

The ENST00000415640.1(MAP4K3-DT):​n.73-18954A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.52 in 152,078 control chromosomes in the GnomAD database, including 24,300 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 0.52 (24300 hom., cov: 32)
• Consequence: MAP4K3-DT ENST00000415640.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.852

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.865 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.73-18954A>C		intron_variant	Intron 1 of 2	3
MAP4K3-DT	ENST00000670934.1	n.522-2687A>C		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.520 AC: 78946 AN: 151962 Hom.: 24233 Cov.: 32

Gnomad AFR AF: 0.872

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.520 AC: 79070 AN: 152078 Hom.: 24300 Cov.: 32 AF XY: 0.516 AC XY: 38353 AN XY: 74332

Gnomad4 AFR AF: 0.873

Gnomad4 AMR AF: 0.407

Gnomad4 ASJ AF: 0.313

Gnomad4 EAS AF: 0.423

Gnomad4 SAS AF: 0.451

Gnomad4 FIN AF: 0.389

Gnomad4 NFE AF: 0.376

Gnomad4 OTH AF: 0.483

Alfa AF: 0.452 Hom.: 3037

Bravo AF: 0.537

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.5
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: rs2058619; hg19: chr2-39854448;