3-193815914-A-G

Variant names:

• chr3-193815914-A-G
• rs9814527

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 0.396 in 151,970 control chromosomes in the GnomAD database, including 12,959 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 0.40 (12959 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.245
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.573 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: 0.396 AC: 60167 AN: 151852 Hom.: 12949 Cov.: 32

Gnomad AFR AF: 0.579

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.395

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.396 AC: 60204 AN: 151970 Hom.: 12959 Cov.: 32 AF XY: 0.394 AC XY: 29234 AN XY: 74266

African (AFR) AF: 0.579 AC: 23976 AN: 41422

American (AMR) AF: 0.276 AC: 4225 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1434 AN: 3472

East Asian (EAS) AF: 0.255 AC: 1314 AN: 5156

South Asian (SAS) AF: 0.473 AC: 2274 AN: 4808

European-Finnish (FIN) AF: 0.350 AC: 3700 AN: 10566

Middle Eastern (MID) AF: 0.401 AC: 117 AN: 292

European-Non Finnish (NFE) AF: 0.326 AC: 22141 AN: 67952

Other (OTH) AF: 0.376 AC: 791 AN: 2104

Alfa AF: 0.344 Hom.: 36968

Bravo AF: 0.394

Asia WGS AF: 0.376 AC: 1308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.7
DANN	Benign	0.59
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs9814527; hg19: chr3-193533703;