9-5200714-A-G

Variant names:

• chr9-5200714-A-G
• rs16922786

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 0.309 in 151,778 control chromosomes in the GnomAD database, including 7,443 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 0.31 (7443 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0600
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.366 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: 0.308 AC: 46785 AN: 151660 Hom.: 7433 Cov.: 31

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.309 AC: 46843 AN: 151778 Hom.: 7443 Cov.: 31 AF XY: 0.313 AC XY: 23182 AN XY: 74170

African (AFR) AF: 0.371 AC: 15348 AN: 41358

American (AMR) AF: 0.287 AC: 4373 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 870 AN: 3470

East Asian (EAS) AF: 0.255 AC: 1308 AN: 5136

South Asian (SAS) AF: 0.340 AC: 1631 AN: 4802

European-Finnish (FIN) AF: 0.351 AC: 3695 AN: 10542

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.275 AC: 18669 AN: 67936

Other (OTH) AF: 0.299 AC: 630 AN: 2104

Alfa AF: 0.290 Hom.: 3352

Bravo AF: 0.302

Asia WGS AF: 0.314 AC: 1090 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.7
DANN	Benign	0.74
PhyloP100		0.060

Splicing

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

Other links and lift over

dbSNP: rs16922786; hg19: chr9-5200714; COSMIC: COSV60323468;