rs2120913

Variant names:

• chr5-100732771-A-G
• rs2120913

Your query was ambiguous. Multiple possible variants found:

• chr5-100732771-A-G
• chr5-100732771-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 0.52 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.305 AC: 12658 AN: 41440

American (AMR) AF: 0.509 AC: 7767 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.647 AC: 2248 AN: 3472

East Asian (EAS) AF: 0.628 AC: 3254 AN: 5178

South Asian (SAS) AF: 0.744 AC: 3589 AN: 4824

European-Finnish (FIN) AF: 0.606 AC: 6374 AN: 10520

Middle Eastern (MID) AF: 0.628 AC: 181 AN: 288

European-Non Finnish (NFE) AF: 0.607 AC: 41260 AN: 67928

Other (OTH) AF: 0.544 AC: 1147 AN: 2110

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
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs2120913; hg19: chr5-100068475;