2-39603043-C-T

Variant names:

• chr2-39603043-C-T
• rs2160389
• ENST00000426083.5:n.674-269C>T

Variant summary

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

The ENST00000426083.5(MAP4K3-DT):​n.674-269C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.875 in 152,096 control chromosomes in the GnomAD database, including 60,370 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 0.87 (60370 hom., cov: 31)
• Consequence: MAP4K3-DT ENST00000426083.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.224
• Publications: 0 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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.981 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000426083.5. 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	ENST00000426083.5	TSL:1	n.674-269C>T		intron	N/A
	MAP4K3-DT	ENST00000415640.1	TSL:3	n.73-43219C>T		intron	N/A
	MAP4K3-DT	ENST00000446698.7	TSL:5	n.531-21056C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.875 AC: 132926 AN: 151978 Hom.: 60332 Cov.: 31

Gnomad AFR AF: 0.602

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.920

Gnomad ASJ AF: 0.991

Gnomad EAS AF: 0.956

Gnomad SAS AF: 0.986

Gnomad FIN AF: 0.999

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.987

Gnomad OTH AF: 0.903

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

GnomAD4 genome AF: 0.875 AC: 133021 AN: 152096 Hom.: 60370 Cov.: 31 AF XY: 0.879 AC XY: 65347 AN XY: 74352

African (AFR) AF: 0.603 AC: 24966 AN: 41402

American (AMR) AF: 0.920 AC: 14055 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.991 AC: 3438 AN: 3470

East Asian (EAS) AF: 0.956 AC: 4959 AN: 5186

South Asian (SAS) AF: 0.987 AC: 4757 AN: 4820

European-Finnish (FIN) AF: 0.999 AC: 10587 AN: 10602

Middle Eastern (MID) AF: 0.935 AC: 275 AN: 294

European-Non Finnish (NFE) AF: 0.987 AC: 67166 AN: 68026

Other (OTH) AF: 0.902 AC: 1906 AN: 2112

Alfa AF: 0.954 Hom.: 286546

Bravo AF: 0.854

Asia WGS AF: 0.937 AC: 3258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.91
DANN	Benign	0.67
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs2160389; hg19: chr2-39830183;