XR_007061165.1:n.3652C>T

Variant names:

• chr8-9888288-G-A
• rs17150703
• XR_007061165.1:n.3652C>T

Variant summary

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

The XR_007061165.1(LOC124902056):​n.3652C>T 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 0.0866 in 152,144 control chromosomes in the GnomAD database, including 741 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 0.087 (741 hom., cov: 32)
• Consequence: LOC124902056 XR_007061165.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.199
• Publications: 31 publications found

Genes affected

LOC124902056 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0866 AC: 13161 AN: 152026 Hom.: 737 Cov.: 32

Gnomad AFR AF: 0.0218

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.0675

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.0836

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.100

Gnomad OTH AF: 0.0876

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

GnomAD4 genome AF: 0.0866 AC: 13174 AN: 152144 Hom.: 741 Cov.: 32 AF XY: 0.0895 AC XY: 6660 AN XY: 74382

African (AFR) AF: 0.0218 AC: 904 AN: 41524

American (AMR) AF: 0.121 AC: 1846 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0675 AC: 234 AN: 3468

East Asian (EAS) AF: 0.162 AC: 837 AN: 5172

South Asian (SAS) AF: 0.0837 AC: 403 AN: 4816

European-Finnish (FIN) AF: 0.175 AC: 1849 AN: 10564

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.100 AC: 6807 AN: 67992

Other (OTH) AF: 0.0943 AC: 199 AN: 2110

Alfa AF: 0.0971 Hom.: 1891

Bravo AF: 0.0848

Asia WGS AF: 0.145 AC: 503 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.1
DANN	Benign	0.43
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs17150703; hg19: chr8-9745798;