rs2279977

Variant names:

• chr3-3372902-A-C
• rs2279977
• ENST00000420000.6:n.373+9576T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000420000.6(ENSG00000223727):​n.373+9576T>G variant causes a intron 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: ENSG00000223727 ENST00000420000.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.223
• Publications: 2 publications found

Genes affected

ENSG00000223727 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000223727	ENST00000420000.6	n.373+9576T>G		intron_variant	Intron 3 of 4	4
ENSG00000223727	ENST00000451031.5	n.176-35439T>G		intron_variant	Intron 2 of 5	3
ENSG00000223727	ENST00000455703.1	n.232+9576T>G		intron_variant	Intron 2 of 3	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

African (AFR) AF: 0.330 AC: 13698 AN: 41476

American (AMR) AF: 0.392 AC: 5976 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.521 AC: 1806 AN: 3466

East Asian (EAS) AF: 0.340 AC: 1749 AN: 5150

South Asian (SAS) AF: 0.457 AC: 2198 AN: 4812

European-Finnish (FIN) AF: 0.478 AC: 5054 AN: 10580

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.440 AC: 29869 AN: 67882

Other (OTH) AF: 0.422 AC: 892 AN: 2112

Alfa AF: 0.427 Hom.: 55407

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
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs2279977; hg19: chr3-3414586;