chr2-88824725-T-C

Position:

• chr2-88824725-T-C

Variant summary

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

The ENST00000434790.2(ENSG00000290802):​n.232+251A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 152,102 control chromosomes in the GnomAD database, including 888 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 0.10 (888 hom., cov: 32)
• Consequence: ENST00000434790.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.142 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MALLP2	XR_940348.2	n.232+251A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000434790.2	n.232+251A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15757 AN: 151984 Hom.: 890 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0933

Gnomad ASJ AF: 0.0646

Gnomad EAS AF: 0.0381

Gnomad SAS AF: 0.0721

Gnomad FIN AF: 0.0835

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0945

Gnomad OTH AF: 0.0799

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

GnomAD4 genome AF: 0.104 AC: 15775 AN: 152102 Hom.: 888 Cov.: 32 AF XY: 0.101 AC XY: 7534 AN XY: 74350

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.0933

Gnomad4 ASJ AF: 0.0646

Gnomad4 EAS AF: 0.0384

Gnomad4 SAS AF: 0.0722

Gnomad4 FIN AF: 0.0835

Gnomad4 NFE AF: 0.0945

Gnomad4 OTH AF: 0.0810

Alfa AF: 0.0931 Hom.: 959

Bravo AF: 0.107

Asia WGS AF: 0.0650 AC: 227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.4
DANN	Benign	0.71

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1843217; hg19: chr2-89124238;