rs11265257

Variant names:

• chr1-159699194-C-T
• rs11265257

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;