rs2832190

Positions:

• chr21-29115905-G-A
• chr21-29115905-G-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.93).
• 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/exons	MANE	UniProt
MAP3K7CL	NM_001286617.2	c.-168-14890G>A		intron_variant
MAP3K7CL	NM_001286618.2	c.-39-17401G>A		intron_variant
MAP3K7CL	NM_001286619.2	c.-169+6722G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAP3K7CL	ENST00000341618.8	c.370+23324G>A		intron_variant		1
MAP3K7CL	ENST00000399947.6	c.370+23324G>A		intron_variant		1
MAP3K7CL	ENST00000339024.8	c.-169+6722G>A		intron_variant		2		P1

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

Gnomad4 AFR AF: 0.385

Gnomad4 AMR AF: 0.474

Gnomad4 ASJ AF: 0.425

Gnomad4 EAS AF: 0.636

Gnomad4 SAS AF: 0.361

Gnomad4 FIN AF: 0.460

Gnomad4 NFE AF: 0.472

Gnomad4 OTH AF: 0.470

Alfa AF: 0.461 Hom.: 2064

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

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: rs2832190; hg19: chr21-30488226;