rs17056706

chr5-159343747-C-T

Variant summary

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

The NR_037889.1(LOC285626):n.746-3769C>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 0.436 in 152,010 control chromosomes in the GnomAD database, including 15,210 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 0.44 (15210 hom., cov: 32)
• Consequence: LOC285626 NR_037889.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.622

Genes affected

LOC285626 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC285626	NR_037889.1	n.746-3769C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000515337.1	n.746-3769C>T		intron_variant, non_coding_transcript_variant		2
	ENST00000641150.1	n.325-3769C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66241 AN: 151892 Hom.: 15187 Cov.: 32

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.436 AC: 66330 AN: 152010 Hom.: 15210 Cov.: 32 AF XY: 0.444 AC XY: 32974 AN XY: 74290

Gnomad4 AFR AF: 0.557

Gnomad4 AMR AF: 0.446

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.476

Gnomad4 SAS AF: 0.464

Gnomad4 FIN AF: 0.463

Gnomad4 NFE AF: 0.359

Gnomad4 OTH AF: 0.404

Alfa AF: 0.367 Hom.: 10434

Bravo AF: 0.441

Asia WGS AF: 0.443 AC: 1543 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.48
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17056706; hg19: chr5-158770755;