rs492256

chr17-74608037-T-Achr17-74608037-T-C

Variant summary

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

The NR_158152.1(LOC101928343):n.2503+1411T>A 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 0.593 in 152,132 control chromosomes in the GnomAD database, including 28,822 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 0.59 (28822 hom., cov: 32)
• Consequence: LOC101928343 NR_158152.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38

Genes affected

LOC101928343 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.84 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101928343	NR_158152.1	n.2503+1411T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.593 AC: 90115 AN: 152014 Hom.: 28758 Cov.: 32

Gnomad AFR AF: 0.847

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.570

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.583

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

GnomAD4 genome AF: 0.593 AC: 90241 AN: 152132 Hom.: 28822 Cov.: 32 AF XY: 0.589 AC XY: 43785 AN XY: 74362

Gnomad4 AFR AF: 0.848

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.570

Gnomad4 EAS AF: 0.344

Gnomad4 SAS AF: 0.574

Gnomad4 FIN AF: 0.517

Gnomad4 NFE AF: 0.505

Gnomad4 OTH AF: 0.584

Alfa AF: 0.391 Hom.: 966

Bravo AF: 0.598

Asia WGS AF: 0.489 AC: 1699 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.88
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs492256; hg19: chr17-72604176;