rs1339907

Positions:

• chr10-85190900-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;