rs2058619

Positions:

• chr2-39627308-A-C

Variant summary

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

The ENST00000670934.1(MAP4K3-DT):​n.522-2687A>C variant causes a intron, non coding transcript 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 ENST00000670934.1 intron, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAP4K3-DT	ENST00000670934.1	n.522-2687A>C		intron_variant, non_coding_transcript_variant
MAP4K3-DT	ENST00000415640.1	n.73-18954A>C		intron_variant, non_coding_transcript_variant		3

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;