rs1005427

Variant names:

• chr2-39604090-C-A
• rs1005427
• ENST00000415640.1:n.73-42172C>A

Your query was ambiguous. Multiple possible variants found:

• chr2-39604090-C-A
• chr2-39604090-C-G
• chr2-39604090-C-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.73-42172C>A 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 152,200 control chromosomes in the GnomAD database, including 60,402 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 (60401 hom., cov: 32)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: MAP4K3-DT ENST00000415640.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.217
• 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=-0.97).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAP4K3-DT	ENST00000415640.1	n.73-42172C>A		intron_variant	Intron 1 of 2	3
MAP4K3-DT	ENST00000446698.7	n.531-20009C>A		intron_variant	Intron 5 of 5	5
MAP4K3-DT	ENST00000670934.1	n.522-25905C>A		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.875 AC: 133008 AN: 152080 Hom.: 60363 Cov.: 32

Gnomad AFR AF: 0.602

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.920

Gnomad ASJ AF: 0.991

Gnomad EAS AF: 0.957

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

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.875 AC: 133103 AN: 152198 Hom.: 60401 Cov.: 32 AF XY: 0.879 AC XY: 65405 AN XY: 74428

African (AFR) AF: 0.603 AC: 24991 AN: 41442

American (AMR) AF: 0.920 AC: 14077 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.991 AC: 3440 AN: 3472

East Asian (EAS) AF: 0.957 AC: 4946 AN: 5170

South Asian (SAS) AF: 0.987 AC: 4769 AN: 4832

European-Finnish (FIN) AF: 0.999 AC: 10605 AN: 10620

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

European-Non Finnish (NFE) AF: 0.987 AC: 67179 AN: 68040

Other (OTH) AF: 0.902 AC: 1909 AN: 2116

Alfa AF: 0.899 Hom.: 5674

Bravo AF: 0.854

Asia WGS AF: 0.937 AC: 3256 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.16
DANN	Benign	0.80
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs1005427; hg19: chr2-39831230;