rs10486270

Variant names:

• chr7-8932422-C-G
• rs10486270

Your query was ambiguous. Multiple possible variants found:

• chr7-8932422-C-G
• chr7-8932422-C-T

Variant summary

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

The variant allele was found at a frequency of 0.271 in 151,774 control chromosomes in the GnomAD database, including 6,124 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 0.27 (6124 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.257
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.326 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: 0.271 AC: 41113 AN: 151656 Hom.: 6122 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.0855

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.271 AC: 41141 AN: 151774 Hom.: 6124 Cov.: 32 AF XY: 0.266 AC XY: 19772 AN XY: 74208

African (AFR) AF: 0.177 AC: 7321 AN: 41422

American (AMR) AF: 0.318 AC: 4844 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.349 AC: 1209 AN: 3464

East Asian (EAS) AF: 0.0859 AC: 442 AN: 5144

South Asian (SAS) AF: 0.207 AC: 997 AN: 4818

European-Finnish (FIN) AF: 0.279 AC: 2945 AN: 10550

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.329 AC: 22339 AN: 67846

Other (OTH) AF: 0.296 AC: 623 AN: 2104

Alfa AF: 0.183 Hom.: 422

Bravo AF: 0.271

Asia WGS AF: 0.187 AC: 649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.0
DANN	Benign	0.56
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs10486270; hg19: chr7-8972052;