chr7-123415501-G-A

Variant names:

• chr7-123415501-G-A
• rs805803

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 0.193 in 151,986 control chromosomes in the GnomAD database, including 2,959 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 0.19 (2959 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.22 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: 0.193 AC: 29282 AN: 151868 Hom.: 2955 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.193 AC: 29278 AN: 151986 Hom.: 2959 Cov.: 32 AF XY: 0.190 AC XY: 14138 AN XY: 74262

African (AFR) AF: 0.159 AC: 6589 AN: 41438

American (AMR) AF: 0.158 AC: 2416 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.234 AC: 811 AN: 3470

East Asian (EAS) AF: 0.178 AC: 918 AN: 5160

South Asian (SAS) AF: 0.205 AC: 985 AN: 4812

European-Finnish (FIN) AF: 0.164 AC: 1724 AN: 10536

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.223 AC: 15145 AN: 67984

Other (OTH) AF: 0.189 AC: 400 AN: 2112

Alfa AF: 0.212 Hom.: 2564

Bravo AF: 0.191

Asia WGS AF: 0.178 AC: 619 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.4
DANN	Benign	0.28
PhyloP100		-0.0040

Splicing

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

Other links and lift over

dbSNP: rs805803; hg19: chr7-123055555;