rs974515

Positions:

• chr3-3462176-C-T

Variant summary

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

The ENST00000420000.6(ENSG00000223727):​n.201-79526G>A 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 0.395 in 151,788 control chromosomes in the GnomAD database, including 14,083 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 0.40 (14083 hom., cov: 32)
• Consequence: ENST00000420000.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.225

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.801 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
	ENST00000420000.6	n.201-79526G>A		intron_variant, non_coding_transcript_variant		4
	ENST00000451031.5	n.78-21171G>A		intron_variant, non_coding_transcript_variant		3
	ENST00000455703.1	n.59+21863G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.395 AC: 59939 AN: 151670 Hom.: 14073 Cov.: 32

Gnomad AFR AF: 0.613

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.821

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.395 AC: 60005 AN: 151788 Hom.: 14083 Cov.: 32 AF XY: 0.396 AC XY: 29400 AN XY: 74166

Gnomad4 AFR AF: 0.613

Gnomad4 AMR AF: 0.332

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.821

Gnomad4 SAS AF: 0.377

Gnomad4 FIN AF: 0.266

Gnomad4 NFE AF: 0.277

Gnomad4 OTH AF: 0.361

Alfa AF: 0.337 Hom.: 1258

Bravo AF: 0.411

Asia WGS AF: 0.570 AC: 1981 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.7
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs974515; hg19: chr3-3503860;