rs7808659

chr7-128930184-C-Achr7-128930184-C-T

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 0.274 in 151,858 control chromosomes in the GnomAD database, including 6,123 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 0.27 (6123 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41566 AN: 151742 Hom.: 6122 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.274 AC: 41582 AN: 151858 Hom.: 6123 Cov.: 32 AF XY: 0.276 AC XY: 20507 AN XY: 74212

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.275

Gnomad4 EAS AF: 0.317

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.340

Gnomad4 NFE AF: 0.317

Gnomad4 OTH AF: 0.252

Alfa AF: 0.124 Hom.: 238

Bravo AF: 0.261

Asia WGS AF: 0.303 AC: 1052 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.67
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7808659; hg19: chr7-128570238; COSMIC: COSV58236687;