rs7789066

Variant names:

• chr7-106287306-A-G
• rs7789066

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 0.0821 in 152,110 control chromosomes in the GnomAD database, including 573 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 0.082 (573 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.324
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.122 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: 0.0820 AC: 12457 AN: 151992 Hom.: 569 Cov.: 33

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0724

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0229

Gnomad FIN AF: 0.0645

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0693

Gnomad OTH AF: 0.0948

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

GnomAD4 genome AF: 0.0821 AC: 12491 AN: 152110 Hom.: 573 Cov.: 33 AF XY: 0.0807 AC XY: 6001 AN XY: 74362

African (AFR) AF: 0.125 AC: 5166 AN: 41484

American (AMR) AF: 0.0722 AC: 1104 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 435 AN: 3466

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5180

South Asian (SAS) AF: 0.0236 AC: 113 AN: 4798

European-Finnish (FIN) AF: 0.0645 AC: 683 AN: 10588

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.0693 AC: 4712 AN: 67988

Other (OTH) AF: 0.0943 AC: 199 AN: 2110

Alfa AF: 0.0736 Hom.: 1492

Bravo AF: 0.0842

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	5.3
DANN	Benign	0.78
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs7789066; hg19: chr7-105927752;