21-29111830-T-G

Variant names:

• chr21-29111830-T-G
• rs2832186
• ENST00000341618.8:c.370+19249T>G

Variant summary

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

The NM_020152.4(MAP3K7CL):​c.370+19249T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.496 in 151,994 control chromosomes in the GnomAD database, including 18,829 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 0.50 (18829 hom., cov: 31)
• Consequence: MAP3K7CL NM_020152.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.230

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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAP3K7CL	NM_001286634.2	c.370+19249T>G		intron_variant	Intron 5 of 7		NP_001273563.1
MAP3K7CL	NM_001371369.1	c.370+19249T>G		intron_variant	Intron 6 of 8		NP_001358298.1
MAP3K7CL	NM_020152.4	c.370+19249T>G		intron_variant	Intron 7 of 9		NP_064537.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAP3K7CL	ENST00000341618.8	c.370+19249T>G		intron_variant	Intron 5 of 7	1		ENSP00000343212.4
MAP3K7CL	ENST00000399947.6	c.370+19249T>G		intron_variant	Intron 6 of 8	1		ENSP00000382828.2
MAP3K7CL	ENST00000339024.8	c.-169+2647T>G		intron_variant	Intron 2 of 6	2		ENSP00000345777.4

Frequencies

GnomAD3 genomes AF: 0.496 AC: 75348 AN: 151876 Hom.: 18822 Cov.: 31

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.636

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.514

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.496 AC: 75401 AN: 151994 Hom.: 18829 Cov.: 31 AF XY: 0.494 AC XY: 36690 AN XY: 74272

Gnomad4 AFR AF: 0.461

Gnomad4 AMR AF: 0.511

Gnomad4 ASJ AF: 0.466

Gnomad4 EAS AF: 0.637

Gnomad4 SAS AF: 0.411

Gnomad4 FIN AF: 0.482

Gnomad4 NFE AF: 0.514

Gnomad4 OTH AF: 0.518

Alfa AF: 0.507 Hom.: 3140

Bravo AF: 0.498

Asia WGS AF: 0.517 AC: 1801 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.4
DANN	Benign	0.45

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: rs2832186; hg19: chr21-30484151;