17-5808630-A-G

Position:

• chr17-5808630-A-G

Variant summary

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

The NR_040000.1(LOC339166):​n.795-28551A>G 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 0.413 in 152,076 control chromosomes in the GnomAD database, including 15,677 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 0.41 (15677 hom., cov: 31)
• Consequence: LOC339166 NR_040000.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.187

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.545 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC339166	NR_040000.1	n.795-28551A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000563763.5	n.795-28551A>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62745 AN: 151958 Hom.: 15674 Cov.: 31

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.441

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

GnomAD4 genome AF: 0.413 AC: 62760 AN: 152076 Hom.: 15677 Cov.: 31 AF XY: 0.413 AC XY: 30670 AN XY: 74326

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.512

Gnomad4 ASJ AF: 0.552

Gnomad4 EAS AF: 0.251

Gnomad4 SAS AF: 0.420

Gnomad4 FIN AF: 0.535

Gnomad4 NFE AF: 0.550

Gnomad4 OTH AF: 0.438

Alfa AF: 0.527 Hom.: 40678

Bravo AF: 0.398

Asia WGS AF: 0.354 AC: 1231 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.7
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1008588; hg19: chr17-5711950; COSMIC: COSV73784464;