rs509356

Positions:

• chr8-101488161-G-A
• chr8-101488161-G-C
• chr8-101488161-G-T

Variant summary

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

The ENST00000520268.1(ENSG00000254024):​n.50+4289C>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 0.426 in 152,090 control chromosomes in the GnomAD database, including 15,222 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 0.43 (15222 hom., cov: 33)
• Consequence: ENST00000520268.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.209

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.62 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
	ENST00000520268.1	n.50+4289C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64697 AN: 151972 Hom.: 15196 Cov.: 33

Gnomad AFR AF: 0.613

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.426 AC: 64781 AN: 152090 Hom.: 15222 Cov.: 33 AF XY: 0.425 AC XY: 31568 AN XY: 74318

Gnomad4 AFR AF: 0.613

Gnomad4 AMR AF: 0.436

Gnomad4 ASJ AF: 0.311

Gnomad4 EAS AF: 0.638

Gnomad4 SAS AF: 0.394

Gnomad4 FIN AF: 0.316

Gnomad4 NFE AF: 0.321

Gnomad4 OTH AF: 0.410

Alfa AF: 0.343 Hom.: 4434

Bravo AF: 0.444

Asia WGS AF: 0.532 AC: 1849 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.1
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs509356; hg19: chr8-102500389;