rs2251381

chr21-29158371-T-G

Variant summary

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

The NM_001286620.2(MAP3K7CL):c.133-1570T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 152,044 control chromosomes in the GnomAD database, including 14,872 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 0.44 (14872 hom., cov: 32)
• Consequence: MAP3K7CL NM_001286620.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.262

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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAP3K7CL	NM_001286620.2	c.133-1570T>G		intron_variant		ENST00000399928.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAP3K7CL	ENST00000399928.6	c.133-1570T>G		intron_variant		1	NM_001286620.2	P1

Frequencies

GnomAD3 genomes AF: 0.439 AC: 66726 AN: 151924 Hom.: 14868 Cov.: 32

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.655

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.477

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.439 AC: 66767 AN: 152044 Hom.: 14872 Cov.: 32 AF XY: 0.442 AC XY: 32807 AN XY: 74294

Gnomad4 AFR AF: 0.446

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.502

Gnomad4 EAS AF: 0.302

Gnomad4 SAS AF: 0.469

Gnomad4 FIN AF: 0.477

Gnomad4 NFE AF: 0.432

Gnomad4 OTH AF: 0.415

Alfa AF: 0.438 Hom.: 7731

Bravo AF: 0.438

Asia WGS AF: 0.370 AC: 1283 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	7.2
Dann	Benign	0.66

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: rs2251381; hg19: chr21-30530692;