rs11773597

Variant names:

• chr7-99784828-G-C
• rs11773597

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 0.0464 in 152,252 control chromosomes in the GnomAD database, including 224 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 0.046 (224 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.322
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0669 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0464 AC: 7065 AN: 152134 Hom.: 224 Cov.: 32

Gnomad AFR AF: 0.0127

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0395

Gnomad ASJ AF: 0.0490

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0226

Gnomad FIN AF: 0.0781

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0685

Gnomad OTH AF: 0.0549

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

GnomAD4 genome AF: 0.0464 AC: 7064 AN: 152252 Hom.: 224 Cov.: 32 AF XY: 0.0457 AC XY: 3404 AN XY: 74416

African (AFR) AF: 0.0126 AC: 525 AN: 41554

American (AMR) AF: 0.0395 AC: 604 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0490 AC: 170 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5180

South Asian (SAS) AF: 0.0228 AC: 110 AN: 4826

European-Finnish (FIN) AF: 0.0781 AC: 828 AN: 10598

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0685 AC: 4658 AN: 68006

Other (OTH) AF: 0.0543 AC: 115 AN: 2116

Alfa AF: 0.0580 Hom.: 42

Bravo AF: 0.0432

Asia WGS AF: 0.0110 AC: 38 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.1
DANN	Benign	0.45
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs11773597; hg19: chr7-99382451;