9-111865238-A-G

Variant names:

• chr9-111865238-A-G
• rs7863596

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 0.103 in 152,048 control chromosomes in the GnomAD database, including 1,093 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 0.10 (1093 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.208
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.189 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: 0.103 AC: 15599 AN: 151930 Hom.: 1087 Cov.: 31

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.210

Gnomad AMR AF: 0.0527

Gnomad ASJ AF: 0.0524

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.0621

Gnomad FIN AF: 0.0553

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0682

Gnomad OTH AF: 0.0863

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

GnomAD4 genome AF: 0.103 AC: 15614 AN: 152048 Hom.: 1093 Cov.: 31 AF XY: 0.0999 AC XY: 7426 AN XY: 74304

African (AFR) AF: 0.193 AC: 7985 AN: 41430

American (AMR) AF: 0.0526 AC: 804 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0524 AC: 182 AN: 3472

East Asian (EAS) AF: 0.141 AC: 728 AN: 5164

South Asian (SAS) AF: 0.0619 AC: 298 AN: 4812

European-Finnish (FIN) AF: 0.0553 AC: 585 AN: 10578

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0682 AC: 4640 AN: 67998

Other (OTH) AF: 0.0854 AC: 180 AN: 2108

Alfa AF: 0.0966 Hom.: 164

Bravo AF: 0.108

Asia WGS AF: 0.0880 AC: 307 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.32
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs7863596; hg19: chr9-114627518;