XR_007095916.1:n.364A>G

Variant names:

• chr3-55327405-T-C
• rs358793
• XR_007095916.1:n.364A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007095916.1(LOC124906243):​n.364A>G variant causes a non coding transcript exon 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_007095916.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.55
• Publications: 9 publications found

Genes affected

LOC124906243 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000809970.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000242775	ENST00000809970.1		n.362+24821A>G		intron	N/A

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

African (AFR) AF: 0.568 AC: 23560 AN: 41458

American (AMR) AF: 0.509 AC: 7773 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.635 AC: 2204 AN: 3470

East Asian (EAS) AF: 0.285 AC: 1468 AN: 5148

South Asian (SAS) AF: 0.649 AC: 3132 AN: 4826

European-Finnish (FIN) AF: 0.645 AC: 6810 AN: 10556

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.696 AC: 47303 AN: 67994

Other (OTH) AF: 0.631 AC: 1328 AN: 2106

Alfa AF: 0.668 Hom.: 19044

Bravo AF: 0.604

Asia WGS AF: 0.509 AC: 1770 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.37
DANN	Benign	0.65
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs358793; hg19: chr3-55361433;