rs4308311

chr3-106404067-C-G

Variant summary

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

The ENST00000653375.1(ENSG00000286854):n.588+10433G>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 0.764 in 151,984 control chromosomes in the GnomAD database, including 44,681 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 0.76 (44681 hom., cov: 33)
• Consequence: ENST00000653375.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0270

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 (AFR) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101929485	XR_007095992.1	n.2067+2232G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000653375.1	n.588+10433G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.763 AC: 115943 AN: 151866 Hom.: 44623 Cov.: 33

Gnomad AFR AF: 0.865

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.806

Gnomad ASJ AF: 0.770

Gnomad EAS AF: 0.742

Gnomad SAS AF: 0.659

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.758

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

GnomAD4 genome AF: 0.764 AC: 116065 AN: 151984 Hom.: 44681 Cov.: 33 AF XY: 0.758 AC XY: 56297 AN XY: 74278

Gnomad4 AFR AF: 0.865

Gnomad4 AMR AF: 0.806

Gnomad4 ASJ AF: 0.770

Gnomad4 EAS AF: 0.743

Gnomad4 SAS AF: 0.659

Gnomad4 FIN AF: 0.625

Gnomad4 NFE AF: 0.724

Gnomad4 OTH AF: 0.761

Alfa AF: 0.740 Hom.: 5198

Bravo AF: 0.783

Asia WGS AF: 0.717 AC: 2492 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	1.1
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4308311; hg19: chr3-106122914;