rs4817271

Variant names:

• chr21-29119618-G-A
• rs4817271
• ENST00000341618.8:c.370+27037G>A

Your query was ambiguous. Multiple possible variants found:

• chr21-29119618-G-A
• chr21-29119618-G-C

Variant summary

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

The ENST00000341618.8(MAP3K7CL):​c.370+27037G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 151,218 control chromosomes in the GnomAD database, including 4,598 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 0.23 (4598 hom., cov: 31)
• Consequence: MAP3K7CL ENST00000341618.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.360
• Publications: 5 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000341618.8. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAP3K7CL	NM_001286634.2		c.370+27037G>A		intron	N/A	NP_001273563.1
	MAP3K7CL	NM_001371369.1		c.370+27037G>A		intron	N/A	NP_001358298.1
	MAP3K7CL	NM_020152.4		c.370+27037G>A		intron	N/A	NP_064537.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAP3K7CL	ENST00000341618.8	TSL:1	c.370+27037G>A		intron	N/A	ENSP00000343212.4
	MAP3K7CL	ENST00000399947.6	TSL:1	c.370+27037G>A		intron	N/A	ENSP00000382828.2
	MAP3K7CL	ENST00000339024.8	TSL:2	c.-169+10435G>A		intron	N/A	ENSP00000345777.4

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34644 AN: 151134 Hom.: 4604 Cov.: 31

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.187

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.229 AC: 34631 AN: 151218 Hom.: 4598 Cov.: 31 AF XY: 0.226 AC XY: 16687 AN XY: 73764

African (AFR) AF: 0.103 AC: 4229 AN: 41252

American (AMR) AF: 0.299 AC: 4537 AN: 15168

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 928 AN: 3460

East Asian (EAS) AF: 0.400 AC: 2055 AN: 5138

South Asian (SAS) AF: 0.174 AC: 831 AN: 4788

European-Finnish (FIN) AF: 0.195 AC: 2000 AN: 10264

Middle Eastern (MID) AF: 0.366 AC: 107 AN: 292

European-Non Finnish (NFE) AF: 0.283 AC: 19204 AN: 67854

Other (OTH) AF: 0.272 AC: 570 AN: 2092

Alfa AF: 0.253 Hom.: 1097

Bravo AF: 0.235

Asia WGS AF: 0.268 AC: 934 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.4
DANN	Benign	0.47
PhyloP100		0.36
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: rs4817271; hg19: chr21-30491939;