XR_001745842.2:n.1312+7755G>T

Variant names:

• chr8-23676505-G-T
• rs10503733
• ENST00000835200.1:n.476-3008G>T

Variant summary

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

The XR_001745842.2(LOC107986930):​n.1312+7755G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 152,098 control chromosomes in the GnomAD database, including 5,860 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 0.27 (5860 hom., cov: 32)
• Consequence: LOC107986930 XR_001745842.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.614
• Publications: 28 publications found

Genes affected

ENSG00000308589 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.315 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000835200.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000308589	ENST00000835200.1		n.476-3008G>T		intron	N/A
	ENSG00000308589	ENST00000835201.1		n.1098-3008G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41612 AN: 151980 Hom.: 5857 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.274 AC: 41641 AN: 152098 Hom.: 5860 Cov.: 32 AF XY: 0.282 AC XY: 20987 AN XY: 74330

African (AFR) AF: 0.276 AC: 11454 AN: 41476

American (AMR) AF: 0.303 AC: 4637 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 964 AN: 3470

East Asian (EAS) AF: 0.281 AC: 1453 AN: 5178

South Asian (SAS) AF: 0.329 AC: 1581 AN: 4810

European-Finnish (FIN) AF: 0.379 AC: 4008 AN: 10566

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.245 AC: 16628 AN: 67990

Other (OTH) AF: 0.275 AC: 581 AN: 2114

Alfa AF: 0.250 Hom.: 20218

Bravo AF: 0.266

Asia WGS AF: 0.322 AC: 1121 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.46
DANN	Benign	0.67
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs10503733; hg19: chr8-23534018;