NM_001286620.2:c.248+409G>A

Variant names:

• chr21-29160465-G-A
• rs2832225
• NM_001286620.2:c.248+409G>A

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+409G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,222 control chromosomes in the GnomAD database, including 1,210 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 0.12 (1210 hom., cov: 33)
• Consequence: MAP3K7CL NM_001286620.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0460
• Publications: 3 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=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.148 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+409G>A		intron	N/A	NP_001273549.1
	MAP3K7CL	NM_001286634.2		c.548+409G>A		intron	N/A	NP_001273563.1
	MAP3K7CL	NM_001371369.1		c.548+409G>A		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+409G>A		intron	N/A	ENSP00000382812.1
	MAP3K7CL	ENST00000341618.8	TSL:1	c.548+409G>A		intron	N/A	ENSP00000343212.4
	MAP3K7CL	ENST00000399947.6	TSL:1	c.548+409G>A		intron	N/A	ENSP00000382828.2

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18282 AN: 152104 Hom.: 1207 Cov.: 33

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.0385

Gnomad AMR AF: 0.0931

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.000961

Gnomad SAS AF: 0.0602

Gnomad FIN AF: 0.0823

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.120 AC: 18299 AN: 152222 Hom.: 1210 Cov.: 33 AF XY: 0.115 AC XY: 8553 AN XY: 74410

African (AFR) AF: 0.151 AC: 6276 AN: 41524

American (AMR) AF: 0.0930 AC: 1422 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 431 AN: 3472

East Asian (EAS) AF: 0.000963 AC: 5 AN: 5192

South Asian (SAS) AF: 0.0607 AC: 293 AN: 4828

European-Finnish (FIN) AF: 0.0823 AC: 872 AN: 10590

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8655 AN: 68008

Other (OTH) AF: 0.131 AC: 276 AN: 2110

Alfa AF: 0.123 Hom.: 426

Bravo AF: 0.122

Asia WGS AF: 0.0490 AC: 174 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	6.9
DANN	Benign	0.79
PhyloP100		0.046
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: rs2832225; hg19: chr21-30532786;