rs4732636

Positions:

• chr8-28310063-C-A
• chr8-28310063-C-G
• chr8-28310063-C-T

Variant summary

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

The ENST00000521731.1(ENSG00000253690):​n.230+28963G>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 0.246 in 151,912 control chromosomes in the GnomAD database, including 5,398 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 0.25 (5398 hom., cov: 32)
• Consequence: ENST00000521731.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.641

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.414 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
	ENST00000521731.1	n.230+28963G>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37354 AN: 151796 Hom.: 5398 Cov.: 32

Gnomad AFR AF: 0.0959

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.246 AC: 37358 AN: 151912 Hom.: 5398 Cov.: 32 AF XY: 0.247 AC XY: 18350 AN XY: 74222

Gnomad4 AFR AF: 0.0957

Gnomad4 AMR AF: 0.344

Gnomad4 ASJ AF: 0.313

Gnomad4 EAS AF: 0.429

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.233

Gnomad4 NFE AF: 0.294

Gnomad4 OTH AF: 0.273

Alfa AF: 0.289 Hom.: 6487

Bravo AF: 0.248

Asia WGS AF: 0.372 AC: 1291 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.75
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4732636; hg19: chr8-28167580;