21-29107537-T-G

Position:

• chr21-29107537-T-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+14956T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.519 in 151,968 control chromosomes in the GnomAD database, including 20,590 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 0.52 (20590 hom., cov: 31)
• Consequence: MAP3K7CL NM_020152.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.168

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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAP3K7CL	NM_001286634.2	c.370+14956T>G		intron_variant			NP_001273563.1
MAP3K7CL	NM_001371369.1	c.370+14956T>G		intron_variant			NP_001358298.1
MAP3K7CL	NM_020152.4	c.370+14956T>G		intron_variant			NP_064537.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAP3K7CL	ENST00000341618.8	c.370+14956T>G		intron_variant		1		ENSP00000343212.4
MAP3K7CL	ENST00000399947.6	c.370+14956T>G		intron_variant		1		ENSP00000382828.2
MAP3K7CL	ENST00000496779.5	n.819-1503T>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.519 AC: 78813 AN: 151850 Hom.: 20578 Cov.: 31

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.520

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.635

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.519 AC: 78875 AN: 151968 Hom.: 20590 Cov.: 31 AF XY: 0.516 AC XY: 38325 AN XY: 74296

Gnomad4 AFR AF: 0.541

Gnomad4 AMR AF: 0.520

Gnomad4 ASJ AF: 0.465

Gnomad4 EAS AF: 0.636

Gnomad4 SAS AF: 0.416

Gnomad4 FIN AF: 0.476

Gnomad4 NFE AF: 0.515

Gnomad4 OTH AF: 0.538

Alfa AF: 0.450 Hom.: 2533

Bravo AF: 0.524

Asia WGS AF: 0.522 AC: 1817 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.3
DANN	Benign	0.70

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: rs2832178; hg19: chr21-30479858;