rs2160389

Positions:

• chr2-39603043-C-T

Variant summary

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

The ENST00000426083.5(MAP4K3-DT):​n.674-269C>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 0.875 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.224

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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.981 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	ENST00000426083.5	n.674-269C>T		intron_variant, non_coding_transcript_variant		1
MAP4K3-DT	ENST00000670934.1	n.522-26952C>T		intron_variant, non_coding_transcript_variant
MAP4K3-DT	ENST00000415640.1	n.73-43219C>T		intron_variant, non_coding_transcript_variant		3
MAP4K3-DT	ENST00000446698.6	n.530-21056C>T		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.603

Gnomad4 AMR AF: 0.920

Gnomad4 ASJ AF: 0.991

Gnomad4 EAS AF: 0.956

Gnomad4 SAS AF: 0.987

Gnomad4 FIN AF: 0.999

Gnomad4 NFE AF: 0.987

Gnomad4 OTH AF: 0.902

Alfa AF: 0.972 Hom.: 138458

Bravo AF: 0.854

Asia WGS AF: 0.937 AC: 3258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2160389; hg19: chr2-39830183;