chr2-240896015-G-C

Variant names:

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

Variant summary

Our verdict is Likely benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAB21L4	NM_001085437.3	c.-18C>G		5_prime_UTR_variant	Exon 1 of 5	ENST00000388934.5	NP_001078906.3
MAB21L4	XM_011511877.2	c.-18C>G		5_prime_UTR_variant	Exon 2 of 6		XP_011510179.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAB21L4	ENST00000388934.5	c.-18C>G		5_prime_UTR_variant	Exon 1 of 5	2	NM_001085437.3	ENSP00000373586.4
MAB21L4	ENST00000414499.1	c.-18C>G		5_prime_UTR_variant	Exon 2 of 2	4		ENSP00000390935.1
MAB21L4	ENST00000454476.2	c.-2-46C>G		intron_variant	Intron 1 of 1	5		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

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.0000533

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.2
DANN	Benign	0.65

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;