chr7-84515886-A-C

Variant names:

• chr7-84515886-A-C
• rs11766001

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 0.108 in 151,972 control chromosomes in the GnomAD database, including 1,131 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 0.11 (1131 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.69

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 (NFE) allele frequency at 95% confidence interval = 0.152 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: 0.108 AC: 16470 AN: 151854 Hom.: 1131 Cov.: 32

Gnomad AFR AF: 0.0427

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.0967

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.000581

Gnomad SAS AF: 0.0957

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.108 AC: 16466 AN: 151972 Hom.: 1131 Cov.: 32 AF XY: 0.106 AC XY: 7854 AN XY: 74288

Gnomad4 AFR AF: 0.0426

Gnomad4 AMR AF: 0.0963

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.000582

Gnomad4 SAS AF: 0.0966

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.130

Alfa AF: 0.113 Hom.: 179

Bravo AF: 0.103

Asia WGS AF: 0.0420 AC: 146 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	10
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11766001; hg19: chr7-84145202;