2-39616057-G-T

Variant names:

• chr2-39616057-G-T
• rs7587205
• ENST00000415640.1:n.73-30205G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000415640.1(MAP4K3-DT):​n.73-30205G>T variant causes a intron 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 ENST00000415640.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260
• Publications: 8 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=-0.76).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000415640.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAP4K3-DT	ENST00000415640.1	TSL:3	n.73-30205G>T		intron	N/A
	MAP4K3-DT	ENST00000446698.7	TSL:5	n.531-8042G>T		intron	N/A
	MAP4K3-DT	ENST00000670934.1		n.522-13938G>T		intron	N/A

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

African (AFR) AF: 0.324 AC: 13415 AN: 41466

American (AMR) AF: 0.315 AC: 4807 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.332 AC: 1153 AN: 3468

East Asian (EAS) AF: 0.371 AC: 1920 AN: 5174

South Asian (SAS) AF: 0.435 AC: 2096 AN: 4814

European-Finnish (FIN) AF: 0.376 AC: 3973 AN: 10570

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.366 AC: 24847 AN: 67964

Other (OTH) AF: 0.359 AC: 758 AN: 2112

Alfa AF: 0.304 Hom.: 2905

Bravo AF: 0.346

Asia WGS AF: 0.464 AC: 1612 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	7.9
DANN	Benign	0.76
PhyloP100		-0.026

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7587205;

hg19: chr2-39843197;