chr9-72272787-A-C

Variant names:

• chr9-72272787-A-C
• rs11143230

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 0.26 in 152,176 control chromosomes in the GnomAD database, including 5,937 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 0.26 (5937 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.726

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.33 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: 0.260 AC: 39490 AN: 152058 Hom.: 5941 Cov.: 33

Gnomad AFR AF: 0.0985

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.260 AC: 39490 AN: 152176 Hom.: 5937 Cov.: 33 AF XY: 0.259 AC XY: 19281 AN XY: 74380

African (AFR) AF: 0.0985 AC: 4092 AN: 41538

American (AMR) AF: 0.332 AC: 5067 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.247 AC: 856 AN: 3472

East Asian (EAS) AF: 0.221 AC: 1143 AN: 5178

South Asian (SAS) AF: 0.267 AC: 1287 AN: 4820

European-Finnish (FIN) AF: 0.325 AC: 3435 AN: 10574

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.333 AC: 22660 AN: 68010

Other (OTH) AF: 0.282 AC: 594 AN: 2110

Alfa AF: 0.306 Hom.: 34116

Bravo AF: 0.254

Asia WGS AF: 0.226 AC: 785 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	12
DANN	Benign	0.89
PhyloP100		0.73

Splicing

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

Publications

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Other links and lift over

dbSNP: rs11143230; hg19: chr9-74887703;