rs2509656

Positions:

• chr11-119337866-G-A

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 0.153 in 152,200 control chromosomes in the GnomAD database, including 2,020 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 0.15 (2020 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.209 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: 0.153 AC: 23262 AN: 152082 Hom.: 2017 Cov.: 32

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.0344

Gnomad SAS AF: 0.0573

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.153 AC: 23292 AN: 152200 Hom.: 2020 Cov.: 32 AF XY: 0.153 AC XY: 11379 AN XY: 74404

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.0340

Gnomad4 SAS AF: 0.0576

Gnomad4 FIN AF: 0.196

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.149

Alfa AF: 0.139 Hom.: 1645

Bravo AF: 0.151

Asia WGS AF: 0.0570 AC: 200 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.6
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2509656; hg19: chr11-119208576;