11-69804649-A-G

Variant names:

• chr11-69804649-A-G
• rs4980700

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 0.539 in 152,102 control chromosomes in the GnomAD database, including 22,369 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 0.54 (22369 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.407
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.6 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81975 AN: 151984 Hom.: 22353 Cov.: 34

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.619

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.513

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

GnomAD4 genome AF: 0.539 AC: 82040 AN: 152102 Hom.: 22369 Cov.: 34 AF XY: 0.541 AC XY: 40213 AN XY: 74342

African (AFR) AF: 0.548 AC: 22710 AN: 41476

American (AMR) AF: 0.404 AC: 6179 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 1836 AN: 3470

East Asian (EAS) AF: 0.618 AC: 3198 AN: 5172

South Asian (SAS) AF: 0.464 AC: 2240 AN: 4824

European-Finnish (FIN) AF: 0.658 AC: 6960 AN: 10584

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.544 AC: 36998 AN: 67968

Other (OTH) AF: 0.513 AC: 1082 AN: 2110

Alfa AF: 0.536 Hom.: 87191

Bravo AF: 0.524

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.21
DANN	Benign	0.53
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs4980700; hg19: chr11-69619417;