rs7806473

Variant names:

• chr7-54064878-A-G
• rs7806473

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 0.154 in 152,214 control chromosomes in the GnomAD database, including 2,287 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 0.15 (2287 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.483
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.201 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: 0.154 AC: 23463 AN: 152096 Hom.: 2283 Cov.: 32

Gnomad AFR AF: 0.0518

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.0576

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.154 AC: 23483 AN: 152214 Hom.: 2287 Cov.: 32 AF XY: 0.159 AC XY: 11814 AN XY: 74400

African (AFR) AF: 0.0519 AC: 2155 AN: 41552

American (AMR) AF: 0.163 AC: 2491 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 467 AN: 3472

East Asian (EAS) AF: 0.0577 AC: 299 AN: 5182

South Asian (SAS) AF: 0.157 AC: 757 AN: 4828

European-Finnish (FIN) AF: 0.268 AC: 2832 AN: 10584

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.204 AC: 13894 AN: 67996

Other (OTH) AF: 0.128 AC: 270 AN: 2110

Alfa AF: 0.165 Hom.: 409

Bravo AF: 0.141

Asia WGS AF: 0.110 AC: 384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.67
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs7806473; hg19: chr7-54132571;