rs2509897

Positions:

• chr11-57595144-C-G
• chr11-57595144-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 0.723 in 152,070 control chromosomes in the GnomAD database, including 40,660 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 0.72 (40660 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.756

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.869 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: 0.722 AC: 109780 AN: 151952 Hom.: 40604 Cov.: 31

Gnomad AFR AF: 0.876

Gnomad AMI AF: 0.804

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.763

Gnomad EAS AF: 0.860

Gnomad SAS AF: 0.674

Gnomad FIN AF: 0.700

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.710

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

GnomAD4 genome AF: 0.723 AC: 109895 AN: 152070 Hom.: 40660 Cov.: 31 AF XY: 0.727 AC XY: 54007 AN XY: 74320

Gnomad4 AFR AF: 0.876

Gnomad4 AMR AF: 0.709

Gnomad4 ASJ AF: 0.763

Gnomad4 EAS AF: 0.860

Gnomad4 SAS AF: 0.675

Gnomad4 FIN AF: 0.700

Gnomad4 NFE AF: 0.626

Gnomad4 OTH AF: 0.709

Alfa AF: 0.573 Hom.: 1613

Bravo AF: 0.731

Asia WGS AF: 0.770 AC: 2675 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.31
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: rs2509897; hg19: chr11-57362617;