5-163568749-T-C

Variant names:

• chr5-163568749-T-C
• rs294593

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 0.679 in 151,426 control chromosomes in the GnomAD database, including 35,764 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 0.68 (35764 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.62
• Publications: 1 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 (AFR) allele frequency at 95% confidence interval = 0.726 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: 0.679 AC: 102790 AN: 151308 Hom.: 35726 Cov.: 28

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.730

Gnomad AMR AF: 0.666

Gnomad ASJ AF: 0.774

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.723

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

GnomAD4 genome AF: 0.679 AC: 102883 AN: 151426 Hom.: 35764 Cov.: 28 AF XY: 0.663 AC XY: 49049 AN XY: 73976

African (AFR) AF: 0.733 AC: 30171 AN: 41186

American (AMR) AF: 0.666 AC: 10132 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.774 AC: 2683 AN: 3468

East Asian (EAS) AF: 0.318 AC: 1641 AN: 5160

South Asian (SAS) AF: 0.502 AC: 2409 AN: 4796

European-Finnish (FIN) AF: 0.486 AC: 5053 AN: 10398

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.713 AC: 48420 AN: 67894

Other (OTH) AF: 0.719 AC: 1508 AN: 2098

Alfa AF: 0.689 Hom.: 4265

Bravo AF: 0.696

Asia WGS AF: 0.442 AC: 1539 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	0.070
DANN	Benign	0.59
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs294593; hg19: chr5-162995755;