rs1339907

Variant names:

• chr10-85190900-C-T
• rs1339907

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.246

Gnomad4 AMR AF: 0.239

Gnomad4 ASJ AF: 0.348

Gnomad4 EAS AF: 0.0609

Gnomad4 SAS AF: 0.173

Gnomad4 FIN AF: 0.337

Gnomad4 NFE AF: 0.328

Gnomad4 OTH AF: 0.271

Alfa AF: 0.311 Hom.: 1475

Bravo AF: 0.274

Asia WGS AF: 0.129 AC: 451 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1339907; hg19: chr10-86950656;