rs1339907

Variant names:

• chr10-85190900-C-T
• rs1339907

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 0.283 in 151,714 control chromosomes in the GnomAD database, including 6,333 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 0.28 (6333 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.191
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.325 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: 0.283 AC: 42889 AN: 151598 Hom.: 6331 Cov.: 31

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.0610

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.283 AC: 42909 AN: 151714 Hom.: 6333 Cov.: 31 AF XY: 0.278 AC XY: 20609 AN XY: 74112

African (AFR) AF: 0.246 AC: 10180 AN: 41368

American (AMR) AF: 0.239 AC: 3646 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.348 AC: 1209 AN: 3470

East Asian (EAS) AF: 0.0609 AC: 314 AN: 5156

South Asian (SAS) AF: 0.173 AC: 832 AN: 4812

European-Finnish (FIN) AF: 0.337 AC: 3544 AN: 10520

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.328 AC: 22276 AN: 67834

Other (OTH) AF: 0.271 AC: 571 AN: 2104

Alfa AF: 0.307 Hom.: 2471

Bravo AF: 0.274

Asia WGS AF: 0.129 AC: 451 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.67
DANN	Benign	0.26
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs1339907; hg19: chr10-86950656;