rs1486004

Positions:

• chr8-81513112-T-C

Variant summary

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

The ENST00000524085.2(ENSG00000253859):​n.435-8595T>C 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 0.424 in 151,996 control chromosomes in the GnomAD database, including 16,598 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 0.42 (16598 hom., cov: 32)
• Consequence: ENST00000524085.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.827

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.72 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101927118	XR_001745980.2	n.518-12731T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000524085.2	n.435-8595T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64323 AN: 151878 Hom.: 16549 Cov.: 32

Gnomad AFR AF: 0.727

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.424 AC: 64437 AN: 151996 Hom.: 16598 Cov.: 32 AF XY: 0.420 AC XY: 31197 AN XY: 74290

Gnomad4 AFR AF: 0.727

Gnomad4 AMR AF: 0.421

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.129

Gnomad4 SAS AF: 0.383

Gnomad4 FIN AF: 0.282

Gnomad4 NFE AF: 0.299

Gnomad4 OTH AF: 0.409

Alfa AF: 0.317 Hom.: 8116

Bravo AF: 0.446

Asia WGS AF: 0.301 AC: 1046 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.82
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1486004; hg19: chr8-82425347;