9-27713725-G-T

Variant names:

• chr9-27713725-G-T
• rs1411375
• XM_047424284.1:c.80+2060G>T

Variant summary

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

The XR_007061442.1(LOC124902135):​n.139+2060G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.579 in 152,088 control chromosomes in the GnomAD database, including 26,200 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 0.58 (26200 hom., cov: 32)
• Consequence: LOC124902135 XR_007061442.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.32
• Publications: 1 publications found

Genes affected

LOC124902135 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.771 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: 0.579 AC: 88039 AN: 151970 Hom.: 26168 Cov.: 32

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.625

Gnomad EAS AF: 0.791

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.596

Gnomad OTH AF: 0.585

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

GnomAD4 genome AF: 0.579 AC: 88117 AN: 152088 Hom.: 26200 Cov.: 32 AF XY: 0.588 AC XY: 43687 AN XY: 74342

African (AFR) AF: 0.460 AC: 19081 AN: 41496

American (AMR) AF: 0.671 AC: 10249 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.625 AC: 2169 AN: 3470

East Asian (EAS) AF: 0.792 AC: 4080 AN: 5154

South Asian (SAS) AF: 0.615 AC: 2965 AN: 4820

European-Finnish (FIN) AF: 0.667 AC: 7055 AN: 10582

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.596 AC: 40498 AN: 67972

Other (OTH) AF: 0.584 AC: 1229 AN: 2104

Alfa AF: 0.595 Hom.: 24046

Bravo AF: 0.576

Asia WGS AF: 0.654 AC: 2273 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	7.2
DANN	Benign	0.75
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs1411375; hg19: chr9-27713723;