rs10933514

Positions:

• chr2-240896015-G-A
• chr2-240896015-G-C

Variant summary

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

The NM_001085437.3(MAB21L4):​c.-18C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.498 in 1,429,184 control chromosomes in the GnomAD database, including 180,242 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 0.54 (23253 hom., cov: 34)
  • Exomes 𝑓: 0.49 (156989 hom.)
• Consequence: MAB21L4 NM_001085437.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.940

Genes affected

MAB21L4 (HGNC:26216): (mab-21 like 4)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.721 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAB21L4	NM_001085437.3	c.-18C>T		5_prime_UTR_variant	1/5	ENST00000388934.5
MAB21L4	XM_011511877.2	c.-18C>T		5_prime_UTR_variant	2/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAB21L4	ENST00000388934.5	c.-18C>T		5_prime_UTR_variant	1/5	2	NM_001085437.3	P1
MAB21L4	ENST00000414499.1	c.-18C>T		5_prime_UTR_variant	2/2	4
MAB21L4	ENST00000454476.2	c.-2-46C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81890 AN: 151834 Hom.: 23225 Cov.: 34

Gnomad AFR AF: 0.728

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.491

GnomAD3 exomes AF: 0.478 AC: 31547 AN: 65984 Hom.: 7700 AF XY: 0.474 AC XY: 16082 AN XY: 33898

Gnomad AFR exome AF: 0.737

Gnomad AMR exome AF: 0.345

Gnomad ASJ exome AF: 0.433

Gnomad EAS exome AF: 0.415

Gnomad SAS exome AF: 0.426

Gnomad FIN exome AF: 0.495

Gnomad NFE exome AF: 0.496

Gnomad OTH exome AF: 0.483

GnomAD4 exome AF: 0.493 AC: 629691 AN: 1277232 Hom.: 156989 Cov.: 51 AF XY: 0.491 AC XY: 303601 AN XY: 618138

Gnomad4 AFR exome AF: 0.732

Gnomad4 AMR exome AF: 0.353

Gnomad4 ASJ exome AF: 0.405

Gnomad4 EAS exome AF: 0.369

Gnomad4 SAS exome AF: 0.426

Gnomad4 FIN exome AF: 0.493

Gnomad4 NFE exome AF: 0.499

Gnomad4 OTH exome AF: 0.492

GnomAD4 genome AF: 0.539 AC: 81957 AN: 151952 Hom.: 23253 Cov.: 34 AF XY: 0.532 AC XY: 39528 AN XY: 74254

Gnomad4 AFR AF: 0.728

Gnomad4 AMR AF: 0.376

Gnomad4 ASJ AF: 0.397

Gnomad4 EAS AF: 0.405

Gnomad4 SAS AF: 0.418

Gnomad4 FIN AF: 0.496

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.488

Alfa AF: 0.496 Hom.: 7025

Bravo AF: 0.540

Asia WGS AF: 0.474 AC: 1655 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.3
DANN	Benign	0.78

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: rs10933514; hg19: chr2-241835432; COSMIC: COSV56743518; COSMIC: COSV56743518;