2-240895237-A-G

Position:

• chr2-240895237-A-G

Variant summary

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

The NM_001085437.3(MAB21L4):​c.514+247T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.729 in 152,218 control chromosomes in the GnomAD database, including 41,134 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 0.73 (41134 hom., cov: 34)
• Consequence: MAB21L4 NM_001085437.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.87

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAB21L4	NM_001085437.3	c.514+247T>C		intron_variant		ENST00000388934.5	NP_001078906.3
MAB21L4	XM_011511877.2	c.514+247T>C		intron_variant			XP_011510179.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAB21L4	ENST00000388934.5	c.514+247T>C		intron_variant		2	NM_001085437.3	ENSP00000373586	P1

Frequencies

GnomAD3 genomes AF: 0.729 AC: 110836 AN: 152100 Hom.: 41090 Cov.: 34

Gnomad AFR AF: 0.855

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.599

Gnomad EAS AF: 0.722

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.746

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.695

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

GnomAD4 genome AF: 0.729 AC: 110927 AN: 152218 Hom.: 41134 Cov.: 34 AF XY: 0.723 AC XY: 53832 AN XY: 74416

Gnomad4 AFR AF: 0.855

Gnomad4 AMR AF: 0.592

Gnomad4 ASJ AF: 0.599

Gnomad4 EAS AF: 0.721

Gnomad4 SAS AF: 0.536

Gnomad4 FIN AF: 0.746

Gnomad4 NFE AF: 0.703

Gnomad4 OTH AF: 0.689

Alfa AF: 0.692 Hom.: 17949

Bravo AF: 0.725

Asia WGS AF: 0.648 AC: 2259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.12
DANN	Benign	0.48

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: rs3936203; hg19: chr2-241834654;