rs1495592

Positions:

• chr3-30356076-G-A

Variant summary

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

The XR_427323.4(LOC101927995):​n.1149+5137G>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 0.295 in 152,058 control chromosomes in the GnomAD database, including 6,803 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 0.30 (6803 hom., cov: 32)
• Consequence: LOC101927995 XR_427323.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.417

Genes affected

LOC101927995 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101927995	XR_427323.4	n.1149+5137G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44865 AN: 151938 Hom.: 6796 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.295 AC: 44889 AN: 152058 Hom.: 6803 Cov.: 32 AF XY: 0.295 AC XY: 21948 AN XY: 74306

Gnomad4 AFR AF: 0.293

Gnomad4 AMR AF: 0.405

Gnomad4 ASJ AF: 0.237

Gnomad4 EAS AF: 0.340

Gnomad4 SAS AF: 0.279

Gnomad4 FIN AF: 0.285

Gnomad4 NFE AF: 0.274

Gnomad4 OTH AF: 0.280

Alfa AF: 0.281 Hom.: 1650

Bravo AF: 0.307

Asia WGS AF: 0.333 AC: 1161 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.3
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1495592; hg19: chr3-30397568;