rs1666793

chr5-8539413-T-C

Variant summary

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

The ENST00000657075.1(ENSG00000249782):n.688+5483T>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 0.268 in 152,140 control chromosomes in the GnomAD database, including 5,895 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 0.27 (5895 hom., cov: 33)
• Consequence: ENST00000657075.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0860

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 = 0.396 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374647	XR_925766.3	n.650+5483T>C		intron_variant, non_coding_transcript_variant
LOC105374647	XR_925767.3	n.640+5483T>C		intron_variant, non_coding_transcript_variant
LOC105374647	XR_925768.3	n.472+5483T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000657075.1	n.688+5483T>C		intron_variant, non_coding_transcript_variant
	ENST00000654467.1	n.471+5483T>C		intron_variant, non_coding_transcript_variant
	ENST00000659580.1	n.650+5483T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40710 AN: 152022 Hom.: 5905 Cov.: 33

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.268 AC: 40724 AN: 152140 Hom.: 5895 Cov.: 33 AF XY: 0.265 AC XY: 19676 AN XY: 74382

Gnomad4 AFR AF: 0.346

Gnomad4 AMR AF: 0.191

Gnomad4 ASJ AF: 0.354

Gnomad4 EAS AF: 0.370

Gnomad4 SAS AF: 0.411

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.231

Gnomad4 OTH AF: 0.269

Alfa AF: 0.257 Hom.: 2801

Bravo AF: 0.268

Asia WGS AF: 0.360 AC: 1248 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.4
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1666793; hg19: chr5-8539525;