rs723349

chr2-207312269-C-G

Variant summary

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

The ENST00000412387.5(ENSG00000223725):n.315+20372G>C 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 0.058 in 152,212 control chromosomes in the GnomAD database, including 509 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 0.058 (509 hom., cov: 32)
• Consequence: ENST00000412387.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.637

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000412387.5	n.315+20372G>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0579 AC: 8811 AN: 152092 Hom.: 506 Cov.: 32

Gnomad AFR AF: 0.0499

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0691

Gnomad ASJ AF: 0.0323

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.0428

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0363

Gnomad OTH AF: 0.0669

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

GnomAD4 genome AF: 0.0580 AC: 8823 AN: 152212 Hom.: 509 Cov.: 32 AF XY: 0.0605 AC XY: 4505 AN XY: 74420

Gnomad4 AFR AF: 0.0500

Gnomad4 AMR AF: 0.0696

Gnomad4 ASJ AF: 0.0323

Gnomad4 EAS AF: 0.315

Gnomad4 SAS AF: 0.177

Gnomad4 FIN AF: 0.0428

Gnomad4 NFE AF: 0.0363

Gnomad4 OTH AF: 0.0653

Alfa AF: 0.0436 Hom.: 25

Bravo AF: 0.0606

Asia WGS AF: 0.222 AC: 772 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.27
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs723349; hg19: chr2-208176993;