rs2058619

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

MAP4K3-DT (HGNC:54056): (MAP4K3 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -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
MAP4K3-DT	ENST00000827213.1	n.516-18954A>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

African (AFR) AF: 0.873 AC: 36214 AN: 41492

American (AMR) AF: 0.407 AC: 6217 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.313 AC: 1086 AN: 3470

East Asian (EAS) AF: 0.423 AC: 2188 AN: 5178

South Asian (SAS) AF: 0.451 AC: 2174 AN: 4822

European-Finnish (FIN) AF: 0.389 AC: 4103 AN: 10548

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.376 AC: 25544 AN: 67976

Other (OTH) AF: 0.483 AC: 1020 AN: 2110

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
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs2058619; hg19: chr2-39854448;