chr5-2706507-T-C

Variant names:

• chr5-2706507-T-C
• rs2962594

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 0.586 in 151,810 control chromosomes in the GnomAD database, including 26,569 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 0.59 (26569 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.641 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: 0.587 AC: 88986 AN: 151692 Hom.: 26578 Cov.: 31

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.660

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.677

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.649

Gnomad FIN AF: 0.632

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.646

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.586 AC: 88994 AN: 151810 Hom.: 26569 Cov.: 31 AF XY: 0.585 AC XY: 43392 AN XY: 74178

African (AFR) AF: 0.494 AC: 20439 AN: 41346

American (AMR) AF: 0.563 AC: 8607 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.677 AC: 2349 AN: 3470

East Asian (EAS) AF: 0.369 AC: 1887 AN: 5118

South Asian (SAS) AF: 0.647 AC: 3105 AN: 4800

European-Finnish (FIN) AF: 0.632 AC: 6673 AN: 10560

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.646 AC: 43865 AN: 67920

Other (OTH) AF: 0.605 AC: 1278 AN: 2114

Alfa AF: 0.476 Hom.: 1616

Bravo AF: 0.578

Asia WGS AF: 0.501 AC: 1745 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.34
DANN	Benign	0.70
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2962594; hg19: chr5-2706621;