chr8-23670717-T-C

Variant names:

• chr8-23670717-T-C
• rs10503734
• XR_001745841.2:n.2657T>C

Variant summary

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

The XR_001745841.2(LOC107986930):​n.2657T>C 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 0.0953 in 152,144 control chromosomes in the GnomAD database, including 774 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 0.095 (774 hom., cov: 32)
• Consequence: LOC107986930 XR_001745841.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0900
• Publications: 7 publications found

Genes affected

LOC107986930 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986930	XR_001745841.2	n.2657T>C		non_coding_transcript_exon_variant	Exon 4 of 4
LOC107986930	XR_001745842.2	n.1312+1967T>C		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308589	ENST00000835200.1	n.475+1967T>C		intron_variant	Intron 4 of 4
ENSG00000308589	ENST00000835201.1	n.1097+1967T>C		intron_variant	Intron 3 of 3
ENSG00000308589	ENST00000835202.1	n.*165T>C		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.0953 AC: 14488 AN: 152026 Hom.: 774 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.0818

Gnomad ASJ AF: 0.0735

Gnomad EAS AF: 0.00347

Gnomad SAS AF: 0.0426

Gnomad FIN AF: 0.0526

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.0953 AC: 14496 AN: 152144 Hom.: 774 Cov.: 32 AF XY: 0.0910 AC XY: 6770 AN XY: 74386

African (AFR) AF: 0.112 AC: 4642 AN: 41518

American (AMR) AF: 0.0817 AC: 1248 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0735 AC: 255 AN: 3468

East Asian (EAS) AF: 0.00368 AC: 19 AN: 5170

South Asian (SAS) AF: 0.0424 AC: 205 AN: 4830

European-Finnish (FIN) AF: 0.0526 AC: 557 AN: 10596

Middle Eastern (MID) AF: 0.168 AC: 49 AN: 292

European-Non Finnish (NFE) AF: 0.106 AC: 7216 AN: 67976

Other (OTH) AF: 0.102 AC: 215 AN: 2108

Alfa AF: 0.107 Hom.: 1783

Bravo AF: 0.0991

Asia WGS AF: 0.0380 AC: 130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.9
DANN	Benign	0.69
PhyloP100		0.090

Splicing

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

Other links and lift over

dbSNP: rs10503734; hg19: chr8-23528230;