chr3-5499313-C-T

Variant names:

• chr3-5499313-C-T
• rs10510312

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 0.0397 in 152,250 control chromosomes in the GnomAD database, including 142 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 0.040 (142 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0830
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0891 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: 0.0397 AC: 6037 AN: 152132 Hom.: 142 Cov.: 32

Gnomad AFR AF: 0.0396

Gnomad AMI AF: 0.0943

Gnomad AMR AF: 0.0445

Gnomad ASJ AF: 0.0472

Gnomad EAS AF: 0.0963

Gnomad SAS AF: 0.0286

Gnomad FIN AF: 0.0134

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0382

Gnomad OTH AF: 0.0335

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

GnomAD4 genome AF: 0.0397 AC: 6041 AN: 152250 Hom.: 142 Cov.: 32 AF XY: 0.0382 AC XY: 2841 AN XY: 74458

African (AFR) AF: 0.0396 AC: 1646 AN: 41528

American (AMR) AF: 0.0446 AC: 682 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0472 AC: 164 AN: 3472

East Asian (EAS) AF: 0.0961 AC: 497 AN: 5172

South Asian (SAS) AF: 0.0284 AC: 137 AN: 4828

European-Finnish (FIN) AF: 0.0134 AC: 142 AN: 10620

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0382 AC: 2598 AN: 68012

Other (OTH) AF: 0.0341 AC: 72 AN: 2112

Alfa AF: 0.0417 Hom.: 625

Bravo AF: 0.0430

Asia WGS AF: 0.0520 AC: 183 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.9
DANN	Benign	0.24
PhyloP100		0.083

Splicing

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

Other links and lift over

dbSNP: rs10510312; hg19: chr3-5541000;