rs3787662

Positions:

• chr21-29151972-C-A

Variant summary

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

The NM_001286620.2(MAP3K7CL):​c.132+2722C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,164 control chromosomes in the GnomAD database, including 2,046 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 0.13 (2046 hom., cov: 32)
• Consequence: MAP3K7CL NM_001286620.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.322

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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.276 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAP3K7CL	NM_001286620.2	c.132+2722C>A		intron_variant		ENST00000399928.6	NP_001273549.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAP3K7CL	ENST00000399928.6	c.132+2722C>A		intron_variant		1	NM_001286620.2	ENSP00000382812	P1

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19797 AN: 152046 Hom.: 2046 Cov.: 32

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.0248

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0559

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.130 AC: 19819 AN: 152164 Hom.: 2046 Cov.: 32 AF XY: 0.128 AC XY: 9554 AN XY: 74378

Gnomad4 AFR AF: 0.280

Gnomad4 AMR AF: 0.138

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.144

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.0248

Gnomad4 NFE AF: 0.0558

Gnomad4 OTH AF: 0.114

Alfa AF: 0.124 Hom.: 290

Bravo AF: 0.146

Asia WGS AF: 0.137 AC: 477 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	13
DANN	Benign	0.57

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: rs3787662; hg19: chr21-30524293;