rs304256

chr6-25050736-C-Gchr6-25050736-C-T

Variant summary

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

The ENST00000428903.1(ENSG00000229313):n.79-4227C>G 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 0.574 in 151,954 control chromosomes in the GnomAD database, including 26,764 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 0.57 (26764 hom., cov: 31)
• Consequence: ENST00000428903.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.822

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.717 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
	ENST00000428903.1	n.79-4227C>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.575 AC: 87234 AN: 151836 Hom.: 26754 Cov.: 31

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.588

Gnomad ASJ AF: 0.564

Gnomad EAS AF: 0.737

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.701

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.673

Gnomad OTH AF: 0.566

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

GnomAD4 genome AF: 0.574 AC: 87270 AN: 151954 Hom.: 26764 Cov.: 31 AF XY: 0.577 AC XY: 42863 AN XY: 74264

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.588

Gnomad4 ASJ AF: 0.564

Gnomad4 EAS AF: 0.737

Gnomad4 SAS AF: 0.662

Gnomad4 FIN AF: 0.701

Gnomad4 NFE AF: 0.673

Gnomad4 OTH AF: 0.571

Alfa AF: 0.501 Hom.: 1573

Bravo AF: 0.553

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.56
Dann	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs304256; hg19: chr6-25050964;