chr21-29160755-A-G

Variant names:

• chr21-29160755-A-G
• rs2832227
• NM_001286620.2:c.248+699A>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.248+699A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.22 in 152,090 control chromosomes in the GnomAD database, including 4,526 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 0.22 (4526 hom., cov: 32)
• Consequence: MAP3K7CL NM_001286620.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0910
• Publications: 19 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001286620.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAP3K7CL	NM_001286620.2	MANE Select	c.248+699A>G		intron	N/A	NP_001273549.1
	MAP3K7CL	NM_001286634.2		c.548+699A>G		intron	N/A	NP_001273563.1
	MAP3K7CL	NM_001371369.1		c.548+699A>G		intron	N/A	NP_001358298.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAP3K7CL	ENST00000399928.6	TSL:1 MANE Select	c.248+699A>G		intron	N/A	ENSP00000382812.1
	MAP3K7CL	ENST00000341618.8	TSL:1	c.548+699A>G		intron	N/A	ENSP00000343212.4
	MAP3K7CL	ENST00000399947.6	TSL:1	c.548+699A>G		intron	N/A	ENSP00000382828.2

Frequencies

GnomAD3 genomes AF: 0.220 AC: 33439 AN: 151972 Hom.: 4513 Cov.: 32

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.0912

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.220 AC: 33486 AN: 152090 Hom.: 4526 Cov.: 32 AF XY: 0.217 AC XY: 16164 AN XY: 74372

African (AFR) AF: 0.374 AC: 15498 AN: 41436

American (AMR) AF: 0.210 AC: 3212 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 648 AN: 3472

East Asian (EAS) AF: 0.174 AC: 902 AN: 5170

South Asian (SAS) AF: 0.277 AC: 1335 AN: 4822

European-Finnish (FIN) AF: 0.0912 AC: 966 AN: 10596

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.151 AC: 10270 AN: 67996

Other (OTH) AF: 0.209 AC: 441 AN: 2114

Alfa AF: 0.172 Hom.: 1389

Bravo AF: 0.232

Asia WGS AF: 0.259 AC: 900 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.1
DANN	Benign	0.42
PhyloP100		-0.091
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: rs2832227; hg19: chr21-30533076;