rs17150703

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902056	XR_007061165.1	n.3652C>T		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;