2-220366311-A-G

Position:

• chr2-220366311-A-G

Variant summary

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

The ENST00000432993.1(ENSG00000239498):​n.427+44090A>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 0.57 in 151,970 control chromosomes in the GnomAD database, including 25,239 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 0.57 (25239 hom., cov: 32)
• Consequence: ENST00000432993.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.783

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) 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
LOC105373893	XR_001739889.2	n.394+44090A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000432993.1	n.427+44090A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86474 AN: 151850 Hom.: 25187 Cov.: 32

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.672

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.868

Gnomad SAS AF: 0.757

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.570 AC: 86591 AN: 151970 Hom.: 25239 Cov.: 32 AF XY: 0.581 AC XY: 43160 AN XY: 74268

Gnomad4 AFR AF: 0.509

Gnomad4 AMR AF: 0.550

Gnomad4 ASJ AF: 0.576

Gnomad4 EAS AF: 0.869

Gnomad4 SAS AF: 0.759

Gnomad4 FIN AF: 0.673

Gnomad4 NFE AF: 0.558

Gnomad4 OTH AF: 0.567

Alfa AF: 0.560 Hom.: 2981

Bravo AF: 0.555

Asia WGS AF: 0.777 AC: 2702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.11
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1378011; hg19: chr2-221231032;