rs4679351

Positions:

• chr3-127214399-G-A

Variant summary

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

The ENST00000654542.1(ENSG00000287784):​n.84+3991C>T 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 0.747 in 152,096 control chromosomes in the GnomAD database, including 44,348 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 0.75 (44348 hom., cov: 33)
• Consequence: ENST00000654542.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.291

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 (NFE) allele frequency at 95% confidence interval = 0.839 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000654542.1	n.84+3991C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.747 AC: 113510 AN: 151978 Hom.: 44336 Cov.: 33

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.917

Gnomad AMR AF: 0.834

Gnomad ASJ AF: 0.803

Gnomad EAS AF: 0.839

Gnomad SAS AF: 0.832

Gnomad FIN AF: 0.861

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.845

Gnomad OTH AF: 0.773

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

GnomAD4 genome AF: 0.747 AC: 113560 AN: 152096 Hom.: 44348 Cov.: 33 AF XY: 0.752 AC XY: 55880 AN XY: 74346

Gnomad4 AFR AF: 0.492

Gnomad4 AMR AF: 0.835

Gnomad4 ASJ AF: 0.803

Gnomad4 EAS AF: 0.839

Gnomad4 SAS AF: 0.834

Gnomad4 FIN AF: 0.861

Gnomad4 NFE AF: 0.845

Gnomad4 OTH AF: 0.770

Alfa AF: 0.810 Hom.: 8650

Bravo AF: 0.733

Asia WGS AF: 0.787 AC: 2737 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	4.5
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4679351; hg19: chr3-126933242;