rs2832236

Variant names:

• chr21-29175281-A-G
• rs2832236
• NM_001286620.2:c.*389A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MAP3K7CL	NM_001286620.2	c.*389A>G		3_prime_UTR_variant	Exon 5 of 5	ENST00000399928.6	NP_001273549.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAP3K7CL	ENST00000399928.6	c.*389A>G		3_prime_UTR_variant	Exon 5 of 5	1	NM_001286620.2	ENSP00000382812.1

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

African (AFR) AF: 0.807 AC: 92 AN: 114

American (AMR) AF: 0.484 AC: 60 AN: 124

Ashkenazi Jewish (ASJ) AF: 0.579 AC: 66 AN: 114

East Asian (EAS) AF: 0.333 AC: 26 AN: 78

South Asian (SAS) AF: 0.678 AC: 61 AN: 90

European-Finnish (FIN) AF: 0.500 AC: 34 AN: 68

Middle Eastern (MID) AF: 0.375 AC: 6 AN: 16

European-Non Finnish (NFE) AF: 0.518 AC: 1118 AN: 2160

Other (OTH) AF: 0.546 AC: 107 AN: 196

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

African (AFR) AF: 0.752 AC: 31207 AN: 41476

American (AMR) AF: 0.537 AC: 8203 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.587 AC: 2034 AN: 3468

East Asian (EAS) AF: 0.399 AC: 2063 AN: 5174

South Asian (SAS) AF: 0.616 AC: 2966 AN: 4812

European-Finnish (FIN) AF: 0.542 AC: 5715 AN: 10542

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.527 AC: 35820 AN: 67962

Other (OTH) AF: 0.556 AC: 1176 AN: 2114

Alfa AF: 0.553 Hom.: 19069

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
PhyloP100		0.58
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2832236; hg19: chr21-30547602;