rs2832225

chr21-29160465-G-A

Variant summary

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

The NM_001286620.2(MAP3K7CL):c.248+409G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,222 control chromosomes in the GnomAD database, including 1,210 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 0.12 (1210 hom., cov: 33)
• Consequence: MAP3K7CL NM_001286620.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0460

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=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.148 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAP3K7CL	NM_001286620.2	c.248+409G>A		intron_variant		ENST00000399928.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAP3K7CL	ENST00000399928.6	c.248+409G>A		intron_variant		1	NM_001286620.2	P1

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18282 AN: 152104 Hom.: 1207 Cov.: 33

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.0385

Gnomad AMR AF: 0.0931

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.000961

Gnomad SAS AF: 0.0602

Gnomad FIN AF: 0.0823

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.120 AC: 18299 AN: 152222 Hom.: 1210 Cov.: 33 AF XY: 0.115 AC XY: 8553 AN XY: 74410

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.0930

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.000963

Gnomad4 SAS AF: 0.0607

Gnomad4 FIN AF: 0.0823

Gnomad4 NFE AF: 0.127

Gnomad4 OTH AF: 0.131

Alfa AF: 0.129 Hom.: 257

Bravo AF: 0.122

Asia WGS AF: 0.0490 AC: 174 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
Cadd	Benign	6.9
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: rs2832225; hg19: chr21-30532786;