11-97628847-C-G

Variant names:

• chr11-97628847-C-G
• rs1477627

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 0.321 in 151,610 control chromosomes in the GnomAD database, including 8,091 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 0.32 (8091 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48616 AN: 151492 Hom.: 8090 Cov.: 32

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.321 AC: 48624 AN: 151610 Hom.: 8091 Cov.: 32 AF XY: 0.319 AC XY: 23602 AN XY: 74072

African (AFR) AF: 0.263 AC: 10902 AN: 41400

American (AMR) AF: 0.303 AC: 4595 AN: 15168

Ashkenazi Jewish (ASJ) AF: 0.332 AC: 1149 AN: 3464

East Asian (EAS) AF: 0.185 AC: 945 AN: 5118

South Asian (SAS) AF: 0.362 AC: 1746 AN: 4826

European-Finnish (FIN) AF: 0.339 AC: 3572 AN: 10530

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.363 AC: 24630 AN: 67794

Other (OTH) AF: 0.316 AC: 664 AN: 2104

Alfa AF: 0.203 Hom.: 451

Bravo AF: 0.315

Asia WGS AF: 0.298 AC: 1031 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.42
DANN	Benign	0.76
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1477627; hg19: chr11-97499847;