rs7027110

Variant names:

• chr9-106836765-G-A
• rs7027110

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 0.199 in 152,108 control chromosomes in the GnomAD database, including 3,069 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 0.20 (3069 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0320

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.248 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: 0.199 AC: 30211 AN: 151990 Hom.: 3068 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.199 AC: 30218 AN: 152108 Hom.: 3069 Cov.: 32 AF XY: 0.198 AC XY: 14711 AN XY: 74378

Gnomad4 AFR AF: 0.167

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.173

Gnomad4 SAS AF: 0.260

Gnomad4 FIN AF: 0.210

Gnomad4 NFE AF: 0.223

Gnomad4 OTH AF: 0.196

Alfa AF: 0.220 Hom.: 5819

Bravo AF: 0.193

Asia WGS AF: 0.243 AC: 845 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.9
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7027110; hg19: chr9-109599046;