rs661204

Variant names:

• chr11-69516215-G-A
• rs661204

Your query was ambiguous. Multiple possible variants found:

• chr11-69516215-G-A
• chr11-69516215-G-C

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 0.119 in 152,192 control chromosomes in the GnomAD database, including 1,181 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 0.12 (1181 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.153 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: 0.119 AC: 18094 AN: 152074 Hom.: 1180 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.0832

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.00751

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.119 AC: 18111 AN: 152192 Hom.: 1181 Cov.: 32 AF XY: 0.121 AC XY: 8996 AN XY: 74412

African (AFR) AF: 0.126 AC: 5211 AN: 41522

American (AMR) AF: 0.0831 AC: 1271 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 450 AN: 3472

East Asian (EAS) AF: 0.00715 AC: 37 AN: 5178

South Asian (SAS) AF: 0.163 AC: 784 AN: 4820

European-Finnish (FIN) AF: 0.144 AC: 1524 AN: 10592

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8476 AN: 67992

Other (OTH) AF: 0.117 AC: 247 AN: 2110

Alfa AF: 0.120 Hom.: 151

Bravo AF: 0.110

Asia WGS AF: 0.107 AC: 373 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.2
DANN	Benign	0.098
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs661204; hg19: chr11-69330983;