5-34628522-C-T

Variant names:

• chr5-34628522-C-T
• rs409045

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 0.662 in 152,032 control chromosomes in the GnomAD database, including 33,497 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 0.66 (33497 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.824 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: 0.662 AC: 100616 AN: 151914 Hom.: 33461 Cov.: 31

Gnomad AFR AF: 0.657

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.649

Gnomad EAS AF: 0.845

Gnomad SAS AF: 0.815

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.641

Gnomad OTH AF: 0.677

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

GnomAD4 genome AF: 0.662 AC: 100708 AN: 152032 Hom.: 33497 Cov.: 31 AF XY: 0.667 AC XY: 49533 AN XY: 74292

African (AFR) AF: 0.657 AC: 27239 AN: 41456

American (AMR) AF: 0.680 AC: 10380 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.649 AC: 2251 AN: 3470

East Asian (EAS) AF: 0.845 AC: 4360 AN: 5158

South Asian (SAS) AF: 0.815 AC: 3924 AN: 4816

European-Finnish (FIN) AF: 0.657 AC: 6940 AN: 10566

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.641 AC: 43586 AN: 67974

Other (OTH) AF: 0.675 AC: 1425 AN: 2112

Alfa AF: 0.655 Hom.: 66142

Bravo AF: 0.662

Asia WGS AF: 0.798 AC: 2775 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.3
DANN	Benign	0.40
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs409045; hg19: chr5-34628627;