rs1330645

Variant names:

• chr5-26070518-A-G
• rs1330645

Your query was ambiguous. Multiple possible variants found:

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

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 0.41 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
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.208 AC: 8616 AN: 41400

American (AMR) AF: 0.351 AC: 5323 AN: 15166

Ashkenazi Jewish (ASJ) AF: 0.560 AC: 1940 AN: 3464

East Asian (EAS) AF: 0.119 AC: 611 AN: 5152

South Asian (SAS) AF: 0.587 AC: 2836 AN: 4832

European-Finnish (FIN) AF: 0.534 AC: 5622 AN: 10522

Middle Eastern (MID) AF: 0.517 AC: 150 AN: 290

European-Non Finnish (NFE) AF: 0.526 AC: 35606 AN: 67718

Other (OTH) AF: 0.424 AC: 895 AN: 2110

Alfa AF: 0.432 Hom.: 1968

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
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs1330645; hg19: chr5-26070627;