rs11265260

Positions:

• chr1-159730249-A-G

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 0.0693 in 152,228 control chromosomes in the GnomAD database, including 446 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 0.069 (446 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.748

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0694 AC: 10551 AN: 152110 Hom.: 444 Cov.: 32

Gnomad AFR AF: 0.0701

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0566

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.0651

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0607

Gnomad OTH AF: 0.0861

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

GnomAD4 genome AF: 0.0693 AC: 10557 AN: 152228 Hom.: 446 Cov.: 32 AF XY: 0.0699 AC XY: 5206 AN XY: 74436

Gnomad4 AFR AF: 0.0704

Gnomad4 AMR AF: 0.0565

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.108

Gnomad4 FIN AF: 0.0651

Gnomad4 NFE AF: 0.0607

Gnomad4 OTH AF: 0.0866

Alfa AF: 0.0664 Hom.: 813

Bravo AF: 0.0684

Asia WGS AF: 0.0900 AC: 311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.3
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: rs11265260; hg19: chr1-159700039;