9-87058705-C-T

Variant names:

• chr9-87058705-C-T
• rs1350564
• XR_007061638.1:n.124+5295C>T

Variant summary

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

The XR_007061638.1(LOC124902196):​n.124+5295C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.497 in 152,002 control chromosomes in the GnomAD database, including 19,532 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 0.50 (19532 hom., cov: 32)
• Consequence: LOC124902196 XR_007061638.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.631
• Publications: 2 publications found

Genes affected

LOC124902196 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.702 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: 0.497 AC: 75511 AN: 151884 Hom.: 19525 Cov.: 32

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.497 AC: 75537 AN: 152002 Hom.: 19532 Cov.: 32 AF XY: 0.496 AC XY: 36850 AN XY: 74316

African (AFR) AF: 0.346 AC: 14355 AN: 41444

American (AMR) AF: 0.607 AC: 9270 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.542 AC: 1881 AN: 3472

East Asian (EAS) AF: 0.721 AC: 3714 AN: 5150

South Asian (SAS) AF: 0.526 AC: 2532 AN: 4816

European-Finnish (FIN) AF: 0.480 AC: 5076 AN: 10574

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.542 AC: 36830 AN: 67974

Other (OTH) AF: 0.541 AC: 1138 AN: 2104

Alfa AF: 0.524 Hom.: 10815

Bravo AF: 0.503

Asia WGS AF: 0.602 AC: 2093 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.2
DANN	Benign	0.51
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs1350564; hg19: chr9-89673620;