3-23052083-T-C

Variant names:

• chr3-23052083-T-C
• rs9310709

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 0.408 in 152,032 control chromosomes in the GnomAD database, including 13,816 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 0.41 (13816 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0200
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.527 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: 0.408 AC: 61976 AN: 151914 Hom.: 13816 Cov.: 32

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.408 AC: 61994 AN: 152032 Hom.: 13816 Cov.: 32 AF XY: 0.414 AC XY: 30760 AN XY: 74318

African (AFR) AF: 0.216 AC: 8947 AN: 41444

American (AMR) AF: 0.536 AC: 8205 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 1588 AN: 3472

East Asian (EAS) AF: 0.454 AC: 2342 AN: 5158

South Asian (SAS) AF: 0.485 AC: 2338 AN: 4816

European-Finnish (FIN) AF: 0.515 AC: 5432 AN: 10556

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.464 AC: 31531 AN: 67968

Other (OTH) AF: 0.434 AC: 916 AN: 2112

Alfa AF: 0.445 Hom.: 66220

Bravo AF: 0.400

Asia WGS AF: 0.460 AC: 1598 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.6
DANN	Benign	0.60
PhyloP100		-0.020

Splicing

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

Other links and lift over

dbSNP: rs9310709; hg19: chr3-23093574;