rs1807909

Variant names:

• chr7-113093816-C-G
• rs1807909

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 0.174 in 131,902 control chromosomes in the GnomAD database, including 1,953 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 0.17 (1953 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.131
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.364 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: 0.174 AC: 22928 AN: 131804 Hom.: 1947 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.174 AC: 22936 AN: 131902 Hom.: 1953 Cov.: 32 AF XY: 0.177 AC XY: 11221 AN XY: 63564

African (AFR) AF: 0.139 AC: 4921 AN: 35408

American (AMR) AF: 0.122 AC: 1427 AN: 11676

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 605 AN: 3160

East Asian (EAS) AF: 0.0999 AC: 428 AN: 4286

South Asian (SAS) AF: 0.379 AC: 1555 AN: 4100

European-Finnish (FIN) AF: 0.165 AC: 1368 AN: 8276

Middle Eastern (MID) AF: 0.164 AC: 40 AN: 244

European-Non Finnish (NFE) AF: 0.196 AC: 12163 AN: 62182

Other (OTH) AF: 0.182 AC: 314 AN: 1726

Alfa AF: 0.166 Hom.: 277

Bravo AF: 0.142

Asia WGS AF: 0.177 AC: 614 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.5
DANN	Benign	0.66
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs1807909; hg19: chr7-112733871;