rs1999321

Positions:

• chr21-29157912-A-C

Variant summary

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

The NM_001286620.2(MAP3K7CL):​c.133-2029A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 152,052 control chromosomes in the GnomAD database, including 24,333 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 0.56 (24333 hom., cov: 32)
• Consequence: MAP3K7CL NM_001286620.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.102

Genes affected

MAP3K7CL (HGNC:16457): (MAP3K7 C-terminal like) Located in cytosol and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

MAP3K7CL (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.644 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAP3K7CL	NM_001286620.2	c.133-2029A>C		intron_variant		ENST00000399928.6	NP_001273549.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAP3K7CL	ENST00000399928.6	c.133-2029A>C		intron_variant		1	NM_001286620.2	ENSP00000382812.1

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85327 AN: 151934 Hom.: 24300 Cov.: 32

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.702

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.562 AC: 85411 AN: 152052 Hom.: 24333 Cov.: 32 AF XY: 0.562 AC XY: 41758 AN XY: 74330

Gnomad4 AFR AF: 0.651

Gnomad4 AMR AF: 0.524

Gnomad4 ASJ AF: 0.568

Gnomad4 EAS AF: 0.399

Gnomad4 SAS AF: 0.616

Gnomad4 FIN AF: 0.544

Gnomad4 NFE AF: 0.526

Gnomad4 OTH AF: 0.538

Alfa AF: 0.529 Hom.: 35290

Bravo AF: 0.563

Asia WGS AF: 0.522 AC: 1812 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.8
DANN	Benign	0.41

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: rs1999321; hg19: chr21-30530233;