2-240896015-G-C

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001085437.3(MAB21L4):​c.-18C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000782 in 1,278,138 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 34)
  • Exomes 𝑓: 7.8e-7 (0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).

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>G		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>G		5_prime_UTR	Exon 1 of 5	ENSP00000373586.4
	MAB21L4	ENST00000414499.1	TSL:4	c.-18C>G		5_prime_UTR	Exon 2 of 2	ENSP00000390935.1
	MAB21L4	ENST00000454476.2	TSL:5	c.-2-46C>G		intron	N/A	ENSP00000394874.2

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome AF: 7.82e-7 AC: 1 AN: 1278138 Hom.: 0 Cov.: 51 AF XY: 0.00000162 AC XY: 1 AN XY: 618556

African (AFR) AF: 0.00 AC: 0 AN: 28188

American (AMR) AF: 0.00 AC: 0 AN: 18602

Ashkenazi Jewish (ASJ) AF: 0.0000533 AC: 1 AN: 18764

East Asian (EAS) AF: 0.00 AC: 0 AN: 34470

South Asian (SAS) AF: 0.00 AC: 0 AN: 61862

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 30706

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3642

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1028720

Other (OTH) AF: 0.00 AC: 0 AN: 53184

GnomAD4 genome Cov.: 34

Alfa AF: 0.00 Hom.: 8007

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.2
DANN	Benign	0.65
PhyloP100		0.94
PromoterAI		0.011	Neutral

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;