rs7701086

Variant names:

• chr5-110055988-A-G
• rs7701086

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 0.265 in 152,008 control chromosomes in the GnomAD database, including 6,295 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 (6295 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.36
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.413 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: 0.265 AC: 40298 AN: 151890 Hom.: 6276 Cov.: 32

Gnomad AFR AF: 0.417

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.265 AC: 40355 AN: 152008 Hom.: 6295 Cov.: 32 AF XY: 0.273 AC XY: 20316 AN XY: 74316

African (AFR) AF: 0.418 AC: 17318 AN: 41430

American (AMR) AF: 0.293 AC: 4475 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 800 AN: 3470

East Asian (EAS) AF: 0.260 AC: 1343 AN: 5156

South Asian (SAS) AF: 0.363 AC: 1747 AN: 4814

European-Finnish (FIN) AF: 0.249 AC: 2639 AN: 10580

Middle Eastern (MID) AF: 0.212 AC: 62 AN: 292

European-Non Finnish (NFE) AF: 0.168 AC: 11388 AN: 67976

Other (OTH) AF: 0.234 AC: 494 AN: 2108

Alfa AF: 0.204 Hom.: 4830

Bravo AF: 0.271

Asia WGS AF: 0.325 AC: 1128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	10
DANN	Benign	0.58
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs7701086; hg19: chr5-109391689; COSMIC: COSV60182452;