chr7-151025080-A-G

Variant names:

• chr7-151025080-A-G
• rs11769158
• XR_007060593.1:n.503-47T>C

Variant summary

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

The XR_007060593.1(LOC124901777):​n.503-47T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.917 in 151,900 control chromosomes in the GnomAD database, including 64,008 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 0.92 (64008 hom., cov: 29)
• Consequence: LOC124901777 XR_007060593.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 2 publications found

Genes affected

LOC124901777 (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 = 0.976 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: 0.917 AC: 139116 AN: 151784 Hom.: 63946 Cov.: 29

Gnomad AFR AF: 0.980

Gnomad AMI AF: 0.896

Gnomad AMR AF: 0.902

Gnomad ASJ AF: 0.873

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.926

Gnomad FIN AF: 0.893

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.881

Gnomad OTH AF: 0.903

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

GnomAD4 genome AF: 0.917 AC: 139236 AN: 151900 Hom.: 64008 Cov.: 29 AF XY: 0.917 AC XY: 68065 AN XY: 74244

African (AFR) AF: 0.980 AC: 40537 AN: 41378

American (AMR) AF: 0.902 AC: 13772 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.873 AC: 3032 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5160 AN: 5166

South Asian (SAS) AF: 0.926 AC: 4436 AN: 4792

European-Finnish (FIN) AF: 0.893 AC: 9425 AN: 10558

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.881 AC: 59883 AN: 67962

Other (OTH) AF: 0.904 AC: 1903 AN: 2104

Alfa AF: 0.905 Hom.: 20122

Bravo AF: 0.922

Asia WGS AF: 0.969 AC: 3369 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	0.29
DANN	Benign	0.67
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs11769158; hg19: chr7-150722167;