rs2832191

Variant names:

• chr21-29116979-A-C
• rs2832191
• ENST00000341618.8:c.370+24398A>C

Your query was ambiguous. Multiple possible variants found:

• chr21-29116979-A-C
• chr21-29116979-A-G
• chr21-29116979-A-T

Variant summary

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

The ENST00000341618.8(MAP3K7CL):​c.370+24398A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.442 in 151,962 control chromosomes in the GnomAD database, including 15,142 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 0.44 (15142 hom., cov: 32)
• Consequence: MAP3K7CL ENST00000341618.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.108
• Publications: 23 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAP3K7CL	NM_001286634.2	c.370+24398A>C		intron_variant	Intron 5 of 7		NP_001273563.1
MAP3K7CL	NM_001371369.1	c.370+24398A>C		intron_variant	Intron 6 of 8		NP_001358298.1
MAP3K7CL	NM_020152.4	c.370+24398A>C		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+24398A>C		intron_variant	Intron 5 of 7	1		ENSP00000343212.4
MAP3K7CL	ENST00000399947.6	c.370+24398A>C		intron_variant	Intron 6 of 8	1		ENSP00000382828.2
MAP3K7CL	ENST00000339024.8	c.-169+7796A>C		intron_variant	Intron 2 of 6	2		ENSP00000345777.4

Frequencies

GnomAD3 genomes AF: 0.443 AC: 67201 AN: 151844 Hom.: 15140 Cov.: 32

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.636

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.442 AC: 67226 AN: 151962 Hom.: 15142 Cov.: 32 AF XY: 0.442 AC XY: 32805 AN XY: 74288

African (AFR) AF: 0.366 AC: 15169 AN: 41470

American (AMR) AF: 0.473 AC: 7212 AN: 15254

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

East Asian (EAS) AF: 0.637 AC: 3296 AN: 5176

South Asian (SAS) AF: 0.363 AC: 1750 AN: 4824

European-Finnish (FIN) AF: 0.461 AC: 4849 AN: 10508

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

European-Non Finnish (NFE) AF: 0.472 AC: 32084 AN: 67938

Other (OTH) AF: 0.466 AC: 985 AN: 2114

Alfa AF: 0.466 Hom.: 52644

Bravo AF: 0.441

Asia WGS AF: 0.489 AC: 1695 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.73
DANN	Benign	0.68
PhyloP100		-0.11
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: rs2832191; hg19: chr21-30489300;