rs7786069

Variant names:

• chr7-65366-G-A
• rs7786069

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 0.243 in 152,100 control chromosomes in the GnomAD database, including 4,445 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 0.24 (4445 hom., cov: 35)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.652
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.461 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: 0.243 AC: 36943 AN: 151982 Hom.: 4445 Cov.: 35

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.243 AC: 36972 AN: 152100 Hom.: 4445 Cov.: 35 AF XY: 0.244 AC XY: 18156 AN XY: 74346

African (AFR) AF: 0.215 AC: 8928 AN: 41520

American (AMR) AF: 0.168 AC: 2568 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 603 AN: 3468

East Asian (EAS) AF: 0.477 AC: 2447 AN: 5134

South Asian (SAS) AF: 0.216 AC: 1042 AN: 4814

European-Finnish (FIN) AF: 0.298 AC: 3153 AN: 10588

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.257 AC: 17449 AN: 67994

Other (OTH) AF: 0.236 AC: 499 AN: 2110

Alfa AF: 0.235 Hom.: 2546

Bravo AF: 0.236

Asia WGS AF: 0.347 AC: 1207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.3
DANN	Benign	0.80
PhyloP100		0.65

Splicing

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

Other links and lift over

dbSNP: rs7786069; hg19: chr7-65366;