rs30740

Variant names:

• chr5-135990901-A-G
• rs30740

Your query was ambiguous. Multiple possible variants found:

• chr5-135990901-A-G
• chr5-135990901-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 0.713 in 152,042 control chromosomes in the GnomAD database, including 38,848 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 0.71 (38848 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.258

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.753 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: 0.713 AC: 108356 AN: 151924 Hom.: 38810 Cov.: 32

Gnomad AFR AF: 0.760

Gnomad AMI AF: 0.775

Gnomad AMR AF: 0.680

Gnomad ASJ AF: 0.795

Gnomad EAS AF: 0.656

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.718

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.710

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

GnomAD4 genome AF: 0.713 AC: 108450 AN: 152042 Hom.: 38848 Cov.: 32 AF XY: 0.713 AC XY: 53022 AN XY: 74316

Gnomad4 AFR AF: 0.760

Gnomad4 AMR AF: 0.680

Gnomad4 ASJ AF: 0.795

Gnomad4 EAS AF: 0.656

Gnomad4 SAS AF: 0.666

Gnomad4 FIN AF: 0.718

Gnomad4 NFE AF: 0.694

Gnomad4 OTH AF: 0.710

Alfa AF: 0.699 Hom.: 36189

Bravo AF: 0.715

Asia WGS AF: 0.676 AC: 2353 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.79
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs30740; hg19: chr5-135326590;