rs2583435

Variant names:

• chr11-2937588-T-C
• rs2583435

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 0.352 in 151,530 control chromosomes in the GnomAD database, including 10,090 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 0.35 (10090 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43
• Publications: 10 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 (EAS) allele frequency at 95% confidence interval = 0.659 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: 0.352 AC: 53267 AN: 151414 Hom.: 10077 Cov.: 31

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.677

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.352 AC: 53313 AN: 151530 Hom.: 10090 Cov.: 31 AF XY: 0.352 AC XY: 26058 AN XY: 73968

African (AFR) AF: 0.377 AC: 15553 AN: 41236

American (AMR) AF: 0.472 AC: 7194 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1257 AN: 3468

East Asian (EAS) AF: 0.677 AC: 3495 AN: 5160

South Asian (SAS) AF: 0.398 AC: 1913 AN: 4812

European-Finnish (FIN) AF: 0.225 AC: 2339 AN: 10406

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.297 AC: 20196 AN: 67912

Other (OTH) AF: 0.376 AC: 792 AN: 2106

Alfa AF: 0.317 Hom.: 2049

Bravo AF: 0.376

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	8.1
DANN	Benign	0.65
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2583435; hg19: chr11-2958818; COSMIC: COSV63085378;