rs11221064

Variant names:

• chr11-127817418-G-C
• rs11221064

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.158 in 151,834 control chromosomes in the GnomAD database, including 1,996 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 0.16 (1996 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.436
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.167 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: 0.158 AC: 24022 AN: 151718 Hom.: 1997 Cov.: 31

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.0398

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.158 AC: 24034 AN: 151834 Hom.: 1996 Cov.: 31 AF XY: 0.157 AC XY: 11612 AN XY: 74190

African (AFR) AF: 0.161 AC: 6671 AN: 41362

American (AMR) AF: 0.137 AC: 2083 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 577 AN: 3468

East Asian (EAS) AF: 0.0401 AC: 206 AN: 5142

South Asian (SAS) AF: 0.171 AC: 824 AN: 4820

European-Finnish (FIN) AF: 0.149 AC: 1567 AN: 10526

Middle Eastern (MID) AF: 0.223 AC: 65 AN: 292

European-Non Finnish (NFE) AF: 0.170 AC: 11538 AN: 67946

Other (OTH) AF: 0.154 AC: 325 AN: 2108

Alfa AF: 0.164 Hom.: 279

Bravo AF: 0.155

Asia WGS AF: 0.0930 AC: 325 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	0.52
DANN	Benign	0.43
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs11221064; hg19: chr11-127687313;