rs2832236

chr21-29175281-A-G

Variant summary

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

The NM_001286620.2(MAP3K7CL):c.*389A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.591 in 154,984 control chromosomes in the GnomAD database, including 27,905 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 0.59 (27481 hom., cov: 32)
  • Exomes 𝑓: 0.53 (424 hom.)
• Consequence: MAP3K7CL NM_001286620.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.577

Genes affected

MAP3K7CL (HGNC:16457): (MAP3K7 C-terminal like) Located in cytosol and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.745 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAP3K7CL	NM_001286620.2	c.*389A>G		3_prime_UTR_variant	5/5	ENST00000399928.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAP3K7CL	ENST00000399928.6	c.*389A>G		3_prime_UTR_variant	5/5	1	NM_001286620.2	P1

Frequencies

GnomAD3 genomes AF: 0.592 AC: 89896 AN: 151904 Hom.: 27443 Cov.: 32

Gnomad AFR AF: 0.752

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.538

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.556

GnomAD4 exome AF: 0.530 AC: 1570 AN: 2960 Hom.: 424 Cov.: 0 AF XY: 0.529 AC XY: 810 AN XY: 1532

Gnomad4 AFR exome AF: 0.807

Gnomad4 AMR exome AF: 0.484

Gnomad4 ASJ exome AF: 0.579

Gnomad4 EAS exome AF: 0.333

Gnomad4 SAS exome AF: 0.678

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.518

Gnomad4 OTH exome AF: 0.546

GnomAD4 genome AF: 0.592 AC: 89987 AN: 152024 Hom.: 27481 Cov.: 32 AF XY: 0.592 AC XY: 43981 AN XY: 74308

Gnomad4 AFR AF: 0.752

Gnomad4 AMR AF: 0.537

Gnomad4 ASJ AF: 0.587

Gnomad4 EAS AF: 0.399

Gnomad4 SAS AF: 0.616

Gnomad4 FIN AF: 0.542

Gnomad4 NFE AF: 0.527

Gnomad4 OTH AF: 0.556

Alfa AF: 0.556 Hom.: 11821

Bravo AF: 0.597

Asia WGS AF: 0.529 AC: 1838 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	4.8
Dann	Benign	0.33

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2832236; hg19: chr21-30547602;