rs2279977

chr3-3372902-A-C

Variant summary

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

The ENST00000420000.6(ENSG00000223727):n.373+9576T>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 0.406 in 151,912 control chromosomes in the GnomAD database, including 12,801 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 0.41 (12801 hom., cov: 32)
• Consequence: ENST00000420000.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.223

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.441 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
	ENST00000420000.6	n.373+9576T>G		intron_variant, non_coding_transcript_variant		4
	ENST00000451031.5	n.176-35439T>G		intron_variant, non_coding_transcript_variant		3
	ENST00000455703.1	n.232+9576T>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.406 AC: 61693 AN: 151792 Hom.: 12788 Cov.: 32

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.521

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.406 AC: 61747 AN: 151912 Hom.: 12801 Cov.: 32 AF XY: 0.409 AC XY: 30363 AN XY: 74256

Gnomad4 AFR AF: 0.330

Gnomad4 AMR AF: 0.392

Gnomad4 ASJ AF: 0.521

Gnomad4 EAS AF: 0.340

Gnomad4 SAS AF: 0.457

Gnomad4 FIN AF: 0.478

Gnomad4 NFE AF: 0.440

Gnomad4 OTH AF: 0.422

Alfa AF: 0.432 Hom.: 24746

Bravo AF: 0.396

Asia WGS AF: 0.379 AC: 1322 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.7
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2279977; hg19: chr3-3414586;