ENST00000341618.8:c.371-24272G>A

Variant names:

• chr21-29124917-G-A
• rs2832195
• ENST00000341618.8:c.371-24272G>A

Variant summary

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

The ENST00000341618.8(MAP3K7CL):​c.371-24272G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 151,964 control chromosomes in the GnomAD database, including 4,791 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 0.23 (4791 hom., cov: 32)
• Consequence: MAP3K7CL ENST00000341618.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590
• Publications: 2 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAP3K7CL	NM_001286634.2	c.371-24272G>A		intron_variant	Intron 5 of 7		NP_001273563.1
MAP3K7CL	NM_001371369.1	c.371-24272G>A		intron_variant	Intron 6 of 8		NP_001358298.1
MAP3K7CL	NM_020152.4	c.371-24272G>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.371-24272G>A		intron_variant	Intron 5 of 7	1		ENSP00000343212.4
MAP3K7CL	ENST00000399947.6	c.371-24272G>A		intron_variant	Intron 6 of 8	1		ENSP00000382828.2
MAP3K7CL	ENST00000460883.5	n.159+2704G>A		intron_variant	Intron 1 of 3	1

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35358 AN: 151846 Hom.: 4793 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.233 AC: 35348 AN: 151964 Hom.: 4791 Cov.: 32 AF XY: 0.230 AC XY: 17078 AN XY: 74262

African (AFR) AF: 0.103 AC: 4281 AN: 41468

American (AMR) AF: 0.302 AC: 4607 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 977 AN: 3468

East Asian (EAS) AF: 0.403 AC: 2082 AN: 5168

South Asian (SAS) AF: 0.194 AC: 932 AN: 4814

European-Finnish (FIN) AF: 0.197 AC: 2077 AN: 10546

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.287 AC: 19528 AN: 67932

Other (OTH) AF: 0.277 AC: 584 AN: 2108

Alfa AF: 0.256 Hom.: 1133

Bravo AF: 0.238

Asia WGS AF: 0.274 AC: 954 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	7.9
DANN	Benign	0.44
PhyloP100		0.059
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: rs2832195; hg19: chr21-30497238;