rs2832159

Positions:

• chr21-29086243-G-A
• chr21-29086243-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000341618.8(MAP3K7CL):​c.57+326G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 152,148 control chromosomes in the GnomAD database, including 3,049 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 0.18 (3049 hom., cov: 32)
• Consequence: MAP3K7CL ENST00000341618.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0600

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=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAP3K7CL	NM_001286617.2	c.-482+326G>A		intron_variant			NP_001273546.1
MAP3K7CL	NM_001286618.2	c.-353+326G>A		intron_variant			NP_001273547.1
MAP3K7CL	NM_001286622.2	c.-406+326G>A		intron_variant			NP_001273551.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAP3K7CL	ENST00000341618.8	c.57+326G>A		intron_variant		1		ENSP00000343212
MAP3K7CL	ENST00000399947.6	c.57+326G>A		intron_variant		1		ENSP00000382828
MAP3K7CL	ENST00000496779.5	n.505+326G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.184 AC: 28018 AN: 152030 Hom.: 3043 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.0887

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.184 AC: 28054 AN: 152148 Hom.: 3049 Cov.: 32 AF XY: 0.179 AC XY: 13317 AN XY: 74390

Gnomad4 AFR AF: 0.298

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.146

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.0887

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.189

Alfa AF: 0.166 Hom.: 403

Bravo AF: 0.197

Asia WGS AF: 0.156 AC: 544 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	9.5
DANN	Benign	0.74

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: rs2832159; hg19: chr21-30458564;