rs2662411

Variant names:

• chr5-10133592-G-A
• rs2662411

Your query was ambiguous. Multiple possible variants found:

• chr5-10133592-G-A
• chr5-10133592-G-C

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 0.532 in 152,054 control chromosomes in the GnomAD database, including 23,598 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 0.53 (23598 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.758
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.798 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: 0.532 AC: 80834 AN: 151936 Hom.: 23549 Cov.: 32

Gnomad AFR AF: 0.761

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.481

Gnomad EAS AF: 0.819

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.532 AC: 80937 AN: 152054 Hom.: 23598 Cov.: 32 AF XY: 0.532 AC XY: 39549 AN XY: 74330

African (AFR) AF: 0.762 AC: 31595 AN: 41472

American (AMR) AF: 0.455 AC: 6954 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.481 AC: 1668 AN: 3468

East Asian (EAS) AF: 0.818 AC: 4241 AN: 5184

South Asian (SAS) AF: 0.544 AC: 2621 AN: 4816

European-Finnish (FIN) AF: 0.390 AC: 4116 AN: 10556

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.413 AC: 28073 AN: 67970

Other (OTH) AF: 0.520 AC: 1097 AN: 2110

Alfa AF: 0.479 Hom.: 6956

Bravo AF: 0.551

Asia WGS AF: 0.673 AC: 2342 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.47
DANN	Benign	0.12
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs2662411; hg19: chr5-10133704;