rs1676232

chr3-117515992-G-A

Variant summary

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

The XR_924361.3(LOC105374056):n.30063+1492G>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 0.474 in 151,936 control chromosomes in the GnomAD database, including 19,742 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 0.47 (19742 hom., cov: 32)
• Consequence: LOC105374056 XR_924361.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14

Genes affected

LOC105374056 (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 (NFE) allele frequency at 95% confidence interval = 0.626 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374056	XR_924361.3	n.30063+1492G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.474 AC: 71998 AN: 151818 Hom.: 19745 Cov.: 32

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.474 AC: 71983 AN: 151936 Hom.: 19742 Cov.: 32 AF XY: 0.471 AC XY: 34919 AN XY: 74214

Gnomad4 AFR AF: 0.207

Gnomad4 AMR AF: 0.418

Gnomad4 ASJ AF: 0.659

Gnomad4 EAS AF: 0.296

Gnomad4 SAS AF: 0.499

Gnomad4 FIN AF: 0.604

Gnomad4 NFE AF: 0.631

Gnomad4 OTH AF: 0.499

Alfa AF: 0.608 Hom.: 53065

Bravo AF: 0.444

Asia WGS AF: 0.393 AC: 1369 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	9.3
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: rs1676232; hg19: chr3-117234839;