2-39616057-G-T

Variant summary

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

The ENST00000670934.1(MAP4K3-DT):n.522-13938G>T 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 0.352 in 152,034 control chromosomes in the GnomAD database, including 9,551 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 0.35 (9551 hom., cov: 32)
• Consequence: MAP4K3-DT ENST00000670934.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260

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=-0.76).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAP4K3-DT	ENST00000670934.1	n.522-13938G>T		intron_variant, non_coding_transcript_variant
MAP4K3-DT	ENST00000415640.1	n.73-30205G>T		intron_variant, non_coding_transcript_variant		3
MAP4K3-DT	ENST00000446698.6	n.530-8042G>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53421 AN: 151916 Hom.: 9536 Cov.: 32

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.392

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.352 AC: 53461 AN: 152034 Hom.: 9551 Cov.: 32 AF XY: 0.353 AC XY: 26239 AN XY: 74308

Gnomad4 AFR AF: 0.324

Gnomad4 AMR AF: 0.315

Gnomad4 ASJ AF: 0.332

Gnomad4 EAS AF: 0.371

Gnomad4 SAS AF: 0.435

Gnomad4 FIN AF: 0.376

Gnomad4 NFE AF: 0.366

Gnomad4 OTH AF: 0.359

Alfa AF: 0.254 Hom.: 862

Bravo AF: 0.346

Asia WGS AF: 0.464 AC: 1612 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
Cadd	Benign	7.9
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7587205; hg19: chr2-39843197;