3-46269575-T-C

Variant names:

• chr3-46269575-T-C
• rs1388603

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 0.543 in 152,096 control chromosomes in the GnomAD database, including 23,379 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 0.54 (23379 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.156
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.887 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: 0.543 AC: 82547 AN: 151978 Hom.: 23349 Cov.: 32

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.909

Gnomad SAS AF: 0.763

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.594

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

GnomAD4 genome AF: 0.543 AC: 82620 AN: 152096 Hom.: 23379 Cov.: 32 AF XY: 0.554 AC XY: 41181 AN XY: 74360

African (AFR) AF: 0.419 AC: 17400 AN: 41488

American (AMR) AF: 0.651 AC: 9947 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.600 AC: 2082 AN: 3468

East Asian (EAS) AF: 0.908 AC: 4706 AN: 5180

South Asian (SAS) AF: 0.763 AC: 3675 AN: 4814

European-Finnish (FIN) AF: 0.547 AC: 5784 AN: 10582

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.545 AC: 37017 AN: 67970

Other (OTH) AF: 0.599 AC: 1263 AN: 2110

Alfa AF: 0.375 Hom.: 995

Bravo AF: 0.543

Asia WGS AF: 0.783 AC: 2721 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.7
DANN	Benign	0.72
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs1388603; hg19: chr3-46311066;