chr2-240896015-G-A

Variant names:

• chr2-240896015-G-A
• rs10933514
• NM_001085437.3:c.-18C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 15 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001085437.3. 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
	MAB21L4	NM_001085437.3	MANE Select	c.-18C>T		5_prime_UTR	Exon 1 of 5	NP_001078906.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAB21L4	ENST00000388934.5	TSL:2 MANE Select	c.-18C>T		5_prime_UTR	Exon 1 of 5	ENSP00000373586.4
	MAB21L4	ENST00000414499.1	TSL:4	c.-18C>T		5_prime_UTR	Exon 2 of 2	ENSP00000390935.1
	MAB21L4	ENST00000454476.2	TSL:5	c.-2-46C>T		intron	N/A	ENSP00000394874.2

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

GnomAD2 exomes AF: 0.478 AC: 31547 AN: 65984 AF XY: 0.474

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 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

African (AFR) AF: 0.732 AC: 20620 AN: 28180

American (AMR) AF: 0.353 AC: 6560 AN: 18586

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 7597 AN: 18758

East Asian (EAS) AF: 0.369 AC: 12722 AN: 34450

South Asian (SAS) AF: 0.426 AC: 26319 AN: 61776

European-Finnish (FIN) AF: 0.493 AC: 15146 AN: 30696

Middle Eastern (MID) AF: 0.437 AC: 1590 AN: 3636

European-Non Finnish (NFE) AF: 0.499 AC: 512987 AN: 1028006

Other (OTH) AF: 0.492 AC: 26150 AN: 53144

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

African (AFR) AF: 0.728 AC: 30183 AN: 41464

American (AMR) AF: 0.376 AC: 5745 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.397 AC: 1377 AN: 3466

East Asian (EAS) AF: 0.405 AC: 2089 AN: 5152

South Asian (SAS) AF: 0.418 AC: 2016 AN: 4820

European-Finnish (FIN) AF: 0.496 AC: 5225 AN: 10542

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.497 AC: 33757 AN: 67904

Other (OTH) AF: 0.488 AC: 1030 AN: 2110

Alfa AF: 0.496 Hom.: 8007

Bravo AF: 0.540

Asia WGS AF: 0.474 AC: 1655 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.3
DANN	Benign	0.78
PhyloP100		0.94
PromoterAI		0.014	Neutral
Mutation Taster		=300/0	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: rs10933514; hg19: chr2-241835432; COSMIC: COSV56743518; COSMIC: COSV56743518;