rs358793

chr3-55327405-T-C

Variant summary

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

The XR_007095917.1(LOC124906243):n.99+23450A>G 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 0.621 in 152,038 control chromosomes in the GnomAD database, including 30,102 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 0.62 (30102 hom., cov: 32)
• Consequence: LOC124906243 XR_007095917.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.55

Genes affected

LOC124906243 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124906243	XR_007095917.1	n.99+23450A>G		intron_variant, non_coding_transcript_variant
LOC124906243	XR_007095916.1	n.364A>G		non_coding_transcript_exon_variant	3/4

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.621 AC: 94279 AN: 151920 Hom.: 30066 Cov.: 32

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.635

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.645

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.631

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

GnomAD4 genome AF: 0.621 AC: 94370 AN: 152038 Hom.: 30102 Cov.: 32 AF XY: 0.613 AC XY: 45548 AN XY: 74312

Gnomad4 AFR AF: 0.568

Gnomad4 AMR AF: 0.509

Gnomad4 ASJ AF: 0.635

Gnomad4 EAS AF: 0.285

Gnomad4 SAS AF: 0.649

Gnomad4 FIN AF: 0.645

Gnomad4 NFE AF: 0.696

Gnomad4 OTH AF: 0.631

Alfa AF: 0.669 Hom.: 17178

Bravo AF: 0.604

Asia WGS AF: 0.509 AC: 1770 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.37
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs358793; hg19: chr3-55361433;