rs4457311

Positions:

• chr8-124272118-G-A

Variant summary

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

The ENST00000668271.1(ENSG00000253227):​n.96+308G>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 0.565 in 152,182 control chromosomes in the GnomAD database, including 24,550 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 0.56 (24550 hom., cov: 34)
• Consequence: ENST00000668271.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.696

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.712 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
	ENST00000668271.1	n.96+308G>A		intron_variant, non_coding_transcript_variant
	ENST00000517482.2	n.144+308G>A		intron_variant, non_coding_transcript_variant		4
	ENST00000660335.1	n.96+308G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.564 AC: 85834 AN: 152064 Hom.: 24513 Cov.: 34

Gnomad AFR AF: 0.591

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.733

Gnomad FIN AF: 0.558

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.565 AC: 85920 AN: 152182 Hom.: 24550 Cov.: 34 AF XY: 0.568 AC XY: 42284 AN XY: 74406

Gnomad4 AFR AF: 0.591

Gnomad4 AMR AF: 0.584

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.563

Gnomad4 SAS AF: 0.732

Gnomad4 FIN AF: 0.558

Gnomad4 NFE AF: 0.541

Gnomad4 OTH AF: 0.539

Alfa AF: 0.561 Hom.: 2352

Bravo AF: 0.565

Asia WGS AF: 0.697 AC: 2420 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.50
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: rs4457311; hg19: chr8-125284359;