ENST00000341618.8:c.370+23324G>A

Variant names:

• chr21-29115905-G-A
• rs2832190
• ENST00000341618.8:c.370+23324G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000341618.8(MAP3K7CL):​c.370+23324G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.448 in 152,080 control chromosomes in the GnomAD database, including 15,440 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 0.45 (15440 hom., cov: 33)
• Consequence: MAP3K7CL ENST00000341618.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.303
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• 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 rank	MANE	Protein	UniProt
MAP3K7CL	NM_001286634.2	c.370+23324G>A		intron_variant	Intron 5 of 7		NP_001273563.1
MAP3K7CL	NM_001371369.1	c.370+23324G>A		intron_variant	Intron 6 of 8		NP_001358298.1
MAP3K7CL	NM_020152.4	c.370+23324G>A		intron_variant	Intron 7 of 9		NP_064537.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAP3K7CL	ENST00000341618.8	c.370+23324G>A		intron_variant	Intron 5 of 7	1		ENSP00000343212.4
MAP3K7CL	ENST00000399947.6	c.370+23324G>A		intron_variant	Intron 6 of 8	1		ENSP00000382828.2
MAP3K7CL	ENST00000339024.8	c.-169+6722G>A		intron_variant	Intron 2 of 6	2		ENSP00000345777.4

Frequencies

GnomAD3 genomes AF: 0.448 AC: 68051 AN: 151962 Hom.: 15439 Cov.: 33

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.635

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.448 AC: 68074 AN: 152080 Hom.: 15440 Cov.: 33 AF XY: 0.447 AC XY: 33215 AN XY: 74338

African (AFR) AF: 0.385 AC: 15957 AN: 41456

American (AMR) AF: 0.474 AC: 7244 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 1476 AN: 3472

East Asian (EAS) AF: 0.636 AC: 3290 AN: 5176

South Asian (SAS) AF: 0.361 AC: 1743 AN: 4826

European-Finnish (FIN) AF: 0.460 AC: 4863 AN: 10570

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.472 AC: 32104 AN: 67978

Other (OTH) AF: 0.470 AC: 994 AN: 2114

Alfa AF: 0.458 Hom.: 2121

Bravo AF: 0.447

Asia WGS AF: 0.487 AC: 1698 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.4
DANN	Benign	0.45
PhyloP100		0.30
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2832190; hg19: chr21-30488226;