rs10266069

Variant names:

• chr7-150652849-A-G
• rs10266069
• XR_007060588.1:n.699-3958T>C

Your query was ambiguous. Multiple possible variants found:

• chr7-150652849-A-G
• chr7-150652849-A-T

Variant summary

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

The XR_007060588.1(LOC124901774):​n.699-3958T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 151,868 control chromosomes in the GnomAD database, including 25,028 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 0.57 (25028 hom., cov: 32)
• Consequence: LOC124901774 XR_007060588.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.992
• Publications: 8 publications found

Genes affected

LOC124901774 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.642 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: 0.569 AC: 86362 AN: 151748 Hom.: 25005 Cov.: 32

Gnomad AFR AF: 0.649

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.513

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.569 AC: 86440 AN: 151868 Hom.: 25028 Cov.: 32 AF XY: 0.575 AC XY: 42687 AN XY: 74186

African (AFR) AF: 0.649 AC: 26837 AN: 41376

American (AMR) AF: 0.574 AC: 8773 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.506 AC: 1755 AN: 3466

East Asian (EAS) AF: 0.513 AC: 2652 AN: 5174

South Asian (SAS) AF: 0.645 AC: 3112 AN: 4822

European-Finnish (FIN) AF: 0.621 AC: 6543 AN: 10528

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.516 AC: 35034 AN: 67912

Other (OTH) AF: 0.531 AC: 1118 AN: 2106

Alfa AF: 0.530 Hom.: 65288

Bravo AF: 0.568

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	6.2
DANN	Benign	0.42
PhyloP100		-0.99

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10266069;

hg19: chr7-150349937;

COSMIC: COSV107155747;