rs1330645

Positions:

• chr5-26070518-A-G
• chr5-26070518-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.41 in 151,564 control chromosomes in the GnomAD database, including 14,778 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 0.41 (14778 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.370

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62170 AN: 151450 Hom.: 14780 Cov.: 32

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.642

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.560

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.410 AC: 62183 AN: 151564 Hom.: 14778 Cov.: 32 AF XY: 0.411 AC XY: 30408 AN XY: 74050

Gnomad4 AFR AF: 0.208

Gnomad4 AMR AF: 0.351

Gnomad4 ASJ AF: 0.560

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.587

Gnomad4 FIN AF: 0.534

Gnomad4 NFE AF: 0.526

Gnomad4 OTH AF: 0.424

Alfa AF: 0.441 Hom.: 1945

Bravo AF: 0.381

Asia WGS AF: 0.371 AC: 1288 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.7
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1330645; hg19: chr5-26070627;