rs3094315

chr1-817186-G-Achr1-817186-G-T

Variant summary

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

The ENST00000447500.4(ENSG00000290784):n.340+187C>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 0.712 in 152,044 control chromosomes in the GnomAD database, including 40,155 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 0.71 (40155 hom., cov: 33)
• Consequence: ENST00000447500.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.780

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.867 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
	ENST00000447500.4	n.340+187C>T		intron_variant, non_coding_transcript_variant		5
	ENST00000634337.2	n.127+10484C>T		intron_variant, non_coding_transcript_variant		5
	ENST00000635509.2	n.100+10484C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.712 AC: 108166 AN: 151926 Hom.: 40145 Cov.: 33

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.784

Gnomad EAS AF: 0.888

Gnomad SAS AF: 0.793

Gnomad FIN AF: 0.797

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.826

Gnomad OTH AF: 0.747

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

GnomAD4 genome AF: 0.712 AC: 108218 AN: 152044 Hom.: 40155 Cov.: 33 AF XY: 0.713 AC XY: 53015 AN XY: 74338

Gnomad4 AFR AF: 0.436

Gnomad4 AMR AF: 0.785

Gnomad4 ASJ AF: 0.784

Gnomad4 EAS AF: 0.888

Gnomad4 SAS AF: 0.791

Gnomad4 FIN AF: 0.797

Gnomad4 NFE AF: 0.826

Gnomad4 OTH AF: 0.749

Alfa AF: 0.804 Hom.: 58451

Asia WGS AF: 0.807 AC: 2807 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.4
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3094315; hg19: chr1-752566;