7-23181020-A-G

Variant names:

• chr7-23181020-A-G
• rs858249

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 0.0903 in 151,886 control chromosomes in the GnomAD database, including 983 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 0.090 (983 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.462
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.186 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0901 AC: 13675 AN: 151768 Hom.: 973 Cov.: 31

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.00659

Gnomad AMR AF: 0.0708

Gnomad ASJ AF: 0.0663

Gnomad EAS AF: 0.0102

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0411

Gnomad OTH AF: 0.0768

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

GnomAD4 genome AF: 0.0903 AC: 13719 AN: 151886 Hom.: 983 Cov.: 31 AF XY: 0.0924 AC XY: 6859 AN XY: 74250

African (AFR) AF: 0.189 AC: 7815 AN: 41338

American (AMR) AF: 0.0712 AC: 1088 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0663 AC: 230 AN: 3470

East Asian (EAS) AF: 0.0100 AC: 52 AN: 5180

South Asian (SAS) AF: 0.104 AC: 502 AN: 4812

European-Finnish (FIN) AF: 0.101 AC: 1063 AN: 10574

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0411 AC: 2794 AN: 67920

Other (OTH) AF: 0.0760 AC: 160 AN: 2106

Alfa AF: 0.0544 Hom.: 1577

Bravo AF: 0.0912

Asia WGS AF: 0.0840 AC: 291 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.96
DANN	Benign	0.49
PhyloP100		-0.46

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs858249; hg19: chr7-23220639;