rs2120913

chr5-100732771-A-Gchr5-100732771-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 0.52 in 151,926 control chromosomes in the GnomAD database, including 22,177 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 0.52 (22177 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.480

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.724 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: 0.521 AC: 79033 AN: 151808 Hom.: 22186 Cov.: 31

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.647

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.746

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.648

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.520 AC: 79031 AN: 151926 Hom.: 22177 Cov.: 31 AF XY: 0.524 AC XY: 38884 AN XY: 74236

Gnomad4 AFR AF: 0.305

Gnomad4 AMR AF: 0.509

Gnomad4 ASJ AF: 0.647

Gnomad4 EAS AF: 0.628

Gnomad4 SAS AF: 0.744

Gnomad4 FIN AF: 0.606

Gnomad4 NFE AF: 0.607

Gnomad4 OTH AF: 0.544

Alfa AF: 0.552 Hom.: 4076

Bravo AF: 0.500

Asia WGS AF: 0.672 AC: 2322 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
Cadd	Benign	2.5
Dann	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2120913; hg19: chr5-100068475;