rs17056704

chr5-159340658-G-Cchr5-159340658-G-T

Variant summary

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

The NR_037889.1(LOC285626):n.746-6858G>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 0.275 in 152,118 control chromosomes in the GnomAD database, including 6,139 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 0.28 (6139 hom., cov: 32)
• Consequence: LOC285626 NR_037889.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0180

Genes affected

LOC285626 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC285626	NR_037889.1	n.746-6858G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000515337.1	n.746-6858G>C		intron_variant, non_coding_transcript_variant		2
	ENST00000641150.1	n.325-6858G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41873 AN: 152000 Hom.: 6140 Cov.: 32

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.275 AC: 41900 AN: 152118 Hom.: 6139 Cov.: 32 AF XY: 0.283 AC XY: 21036 AN XY: 74344

Gnomad4 AFR AF: 0.189

Gnomad4 AMR AF: 0.255

Gnomad4 ASJ AF: 0.253

Gnomad4 EAS AF: 0.282

Gnomad4 SAS AF: 0.322

Gnomad4 FIN AF: 0.412

Gnomad4 NFE AF: 0.310

Gnomad4 OTH AF: 0.243

Alfa AF: 0.183 Hom.: 425

Bravo AF: 0.255

Asia WGS AF: 0.265 AC: 924 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.1
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17056704; hg19: chr5-158767666;