rs4775302

chr15-46347610-G-Achr15-46347610-G-C

Variant summary

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

The ENST00000669454.1(ENSG00000287020):n.391-3744G>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 0.489 in 151,906 control chromosomes in the GnomAD database, including 18,868 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 0.49 (18868 hom., cov: 32)
• Consequence: ENST00000669454.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.38

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.544 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
	ENST00000669454.1	n.391-3744G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.489 AC: 74206 AN: 151788 Hom.: 18862 Cov.: 32

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.489 AC: 74256 AN: 151906 Hom.: 18868 Cov.: 32 AF XY: 0.482 AC XY: 35750 AN XY: 74216

Gnomad4 AFR AF: 0.446

Gnomad4 AMR AF: 0.426

Gnomad4 ASJ AF: 0.588

Gnomad4 EAS AF: 0.207

Gnomad4 SAS AF: 0.404

Gnomad4 FIN AF: 0.491

Gnomad4 NFE AF: 0.549

Gnomad4 OTH AF: 0.496

Alfa AF: 0.517 Hom.: 11542

Bravo AF: 0.481

Asia WGS AF: 0.301 AC: 1048 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	0.11
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4775302; hg19: chr15-46639808; COSMIC: COSV71840654;