rs503897

Variant names:

• chr9-37382102-G-A
• rs503897
• XR_007061477.1:n.680G>A

Your query was ambiguous. Multiple possible variants found:

• chr9-37382102-G-A
• chr9-37382102-G-C

Variant summary

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

The XR_007061477.1(LOC124902153):​n.680G>A 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 0.689 in 152,052 control chromosomes in the GnomAD database, including 37,095 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 0.69 (37095 hom., cov: 32)
• Consequence: LOC124902153 XR_007061477.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.229
• Publications: 4 publications found

Genes affected

LOC124902153 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.829 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: 0.689 AC: 104712 AN: 151934 Hom.: 37059 Cov.: 32

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.629

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.655

Gnomad OTH AF: 0.652

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

GnomAD4 genome AF: 0.689 AC: 104800 AN: 152052 Hom.: 37095 Cov.: 32 AF XY: 0.683 AC XY: 50705 AN XY: 74288

African (AFR) AF: 0.837 AC: 34706 AN: 41482

American (AMR) AF: 0.707 AC: 10808 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.629 AC: 2184 AN: 3470

East Asian (EAS) AF: 0.345 AC: 1784 AN: 5164

South Asian (SAS) AF: 0.527 AC: 2532 AN: 4808

European-Finnish (FIN) AF: 0.584 AC: 6174 AN: 10568

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.655 AC: 44535 AN: 67962

Other (OTH) AF: 0.644 AC: 1361 AN: 2112

Alfa AF: 0.664 Hom.: 143111

Bravo AF: 0.706

Asia WGS AF: 0.493 AC: 1717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.4
DANN	Benign	0.40
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs503897; hg19: chr9-37382099; COSMIC: COSV71913238;