3-86845328-T-C

Variant names:

• chr3-86845328-T-C
• rs9757252

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 0.555 in 151,964 control chromosomes in the GnomAD database, including 23,964 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 0.56 (23964 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.564
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.608 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: 0.555 AC: 84334 AN: 151848 Hom.: 23960 Cov.: 32

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.649

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.704

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.678

Gnomad NFE AF: 0.613

Gnomad OTH AF: 0.554

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

GnomAD4 genome AF: 0.555 AC: 84361 AN: 151964 Hom.: 23964 Cov.: 32 AF XY: 0.555 AC XY: 41223 AN XY: 74268

African (AFR) AF: 0.457 AC: 18953 AN: 41430

American (AMR) AF: 0.476 AC: 7263 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.704 AC: 2440 AN: 3468

East Asian (EAS) AF: 0.463 AC: 2386 AN: 5152

South Asian (SAS) AF: 0.606 AC: 2922 AN: 4818

European-Finnish (FIN) AF: 0.641 AC: 6765 AN: 10560

Middle Eastern (MID) AF: 0.688 AC: 201 AN: 292

European-Non Finnish (NFE) AF: 0.613 AC: 41679 AN: 67954

Other (OTH) AF: 0.549 AC: 1160 AN: 2114

Alfa AF: 0.579 Hom.: 25890

Bravo AF: 0.537

Asia WGS AF: 0.484 AC: 1683 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.0
DANN	Benign	0.56
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs9757252; hg19: chr3-86894478;