rs805803

Variant names:

• chr7-123415501-G-A
• rs805803

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.159

Gnomad4 AMR AF: 0.158

Gnomad4 ASJ AF: 0.234

Gnomad4 EAS AF: 0.178

Gnomad4 SAS AF: 0.205

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.223

Gnomad4 OTH AF: 0.189

Alfa AF: 0.213 Hom.: 1971

Bravo AF: 0.191

Asia WGS AF: 0.178 AC: 619 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs805803; hg19: chr7-123055555;