chr9-107389098-C-T

Variant names:

• chr9-107389098-C-T
• rs1771718

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 0.588 in 146,562 control chromosomes in the GnomAD database, including 26,547 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 0.59 (26547 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.158
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.588 AC: 86128 AN: 146458 Hom.: 26541 Cov.: 32

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.594

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

GnomAD4 genome AF: 0.588 AC: 86156 AN: 146562 Hom.: 26547 Cov.: 32 AF XY: 0.584 AC XY: 41876 AN XY: 71652

African (AFR) AF: 0.378 AC: 13888 AN: 36772

American (AMR) AF: 0.562 AC: 8457 AN: 15054

Ashkenazi Jewish (ASJ) AF: 0.666 AC: 2295 AN: 3446

East Asian (EAS) AF: 0.400 AC: 2006 AN: 5010

South Asian (SAS) AF: 0.465 AC: 2131 AN: 4582

European-Finnish (FIN) AF: 0.725 AC: 7654 AN: 10560

Middle Eastern (MID) AF: 0.597 AC: 172 AN: 288

European-Non Finnish (NFE) AF: 0.703 AC: 47721 AN: 67884

Other (OTH) AF: 0.593 AC: 1221 AN: 2058

Alfa AF: 0.660 Hom.: 15898

Bravo AF: 0.548

Asia WGS AF: 0.419 AC: 1456 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.2
DANN	Benign	0.36
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs1771718; hg19: chr9-110151379;