rs2832160

Positions:

• chr21-29086923-C-T

Variant summary

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

The ENST00000341618.8(MAP3K7CL):​c.57+1006C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,122 control chromosomes in the GnomAD database, including 2,502 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 0.17 (2502 hom., cov: 32)
• Consequence: MAP3K7CL ENST00000341618.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.39

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAP3K7CL	NM_001286617.2	c.-482+1006C>T		intron_variant
MAP3K7CL	NM_001286618.2	c.-353+1006C>T		intron_variant
MAP3K7CL	NM_001286622.2	c.-406+1006C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAP3K7CL	ENST00000341618.8	c.57+1006C>T		intron_variant		1
MAP3K7CL	ENST00000399947.6	c.57+1006C>T		intron_variant		1
MAP3K7CL	ENST00000496779.5	n.505+1006C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26216 AN: 152004 Hom.: 2504 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.0886

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.172 AC: 26228 AN: 152122 Hom.: 2502 Cov.: 32 AF XY: 0.168 AC XY: 12474 AN XY: 74362

Gnomad4 AFR AF: 0.258

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.146

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.0886

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.181

Alfa AF: 0.166 Hom.: 354

Bravo AF: 0.183

Asia WGS AF: 0.151 AC: 528 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.40
DANN	Benign	0.79

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: rs2832160; hg19: chr21-30459244;