NM_001286620.2:c.133-4018A>T

Variant names:

• chr21-29155923-A-T
• rs16983792
• NM_001286620.2:c.133-4018A>T

Variant summary

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

The NM_001286620.2(MAP3K7CL):​c.133-4018A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 152,156 control chromosomes in the GnomAD database, including 2,442 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 0.14 (2442 hom., cov: 32)
• Consequence: MAP3K7CL NM_001286620.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.157

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAP3K7CL	NM_001286620.2	c.133-4018A>T		intron_variant	Intron 3 of 4	ENST00000399928.6	NP_001273549.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAP3K7CL	ENST00000399928.6	c.133-4018A>T		intron_variant	Intron 3 of 4	1	NM_001286620.2	ENSP00000382812.1

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21210 AN: 152038 Hom.: 2441 Cov.: 32

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.0248

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0561

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.140 AC: 21236 AN: 152156 Hom.: 2442 Cov.: 32 AF XY: 0.137 AC XY: 10202 AN XY: 74398

Gnomad4 AFR AF: 0.311

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.0248

Gnomad4 NFE AF: 0.0561

Gnomad4 OTH AF: 0.121

Alfa AF: 0.106 Hom.: 210

Bravo AF: 0.156

Asia WGS AF: 0.139 AC: 482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.7
DANN	Benign	0.67

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: rs16983792; hg19: chr21-30528244;