9-21168307-G-C

Variant names:

• chr9-21168307-G-C
• rs2891157

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 0.612 in 151,800 control chromosomes in the GnomAD database, including 28,619 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 0.61 (28619 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.832 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: 0.612 AC: 92758 AN: 151682 Hom.: 28589 Cov.: 31

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.649

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.852

Gnomad SAS AF: 0.714

Gnomad FIN AF: 0.589

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.602

Gnomad OTH AF: 0.619

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

GnomAD4 genome AF: 0.612 AC: 92838 AN: 151800 Hom.: 28619 Cov.: 31 AF XY: 0.615 AC XY: 45632 AN XY: 74180

African (AFR) AF: 0.577 AC: 23890 AN: 41418

American (AMR) AF: 0.647 AC: 9878 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.611 AC: 2117 AN: 3466

East Asian (EAS) AF: 0.853 AC: 4416 AN: 5178

South Asian (SAS) AF: 0.714 AC: 3441 AN: 4818

European-Finnish (FIN) AF: 0.589 AC: 6193 AN: 10506

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.602 AC: 40813 AN: 67834

Other (OTH) AF: 0.624 AC: 1314 AN: 2106

Alfa AF: 0.593 Hom.: 3220

Bravo AF: 0.614

Asia WGS AF: 0.784 AC: 2725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.37
PhyloP100		-0.046

Splicing

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

Other links and lift over

dbSNP: rs2891157; hg19: chr9-21168306; COSMIC: COSV66518894;