rs11265257

chr1-159699194-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 0.347 in 151,884 control chromosomes in the GnomAD database, including 9,830 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 0.35 (9830 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.562 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: 0.347 AC: 52624 AN: 151766 Hom.: 9826 Cov.: 31

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.347 AC: 52645 AN: 151884 Hom.: 9830 Cov.: 31 AF XY: 0.349 AC XY: 25872 AN XY: 74178

Gnomad4 AFR AF: 0.210

Gnomad4 AMR AF: 0.407

Gnomad4 ASJ AF: 0.383

Gnomad4 EAS AF: 0.579

Gnomad4 SAS AF: 0.340

Gnomad4 FIN AF: 0.390

Gnomad4 NFE AF: 0.389

Gnomad4 OTH AF: 0.364

Alfa AF: 0.341 Hom.: 1356

Bravo AF: 0.341

Asia WGS AF: 0.442 AC: 1538 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.040
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11265257; hg19: chr1-159668984;