rs4553261

Variant names:

• chr10-69616033-A-G
• rs4553261

Your query was ambiguous. Multiple possible variants found:

• chr10-69616033-A-G
• chr10-69616033-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 0.198 in 152,118 control chromosomes in the GnomAD database, including 3,220 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 0.20 (3220 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.402
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.241 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: 0.198 AC: 30140 AN: 152000 Hom.: 3216 Cov.: 33

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.00308

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.198 AC: 30162 AN: 152118 Hom.: 3220 Cov.: 33 AF XY: 0.194 AC XY: 14443 AN XY: 74380

African (AFR) AF: 0.172 AC: 7125 AN: 41486

American (AMR) AF: 0.155 AC: 2369 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 583 AN: 3468

East Asian (EAS) AF: 0.00328 AC: 17 AN: 5188

South Asian (SAS) AF: 0.103 AC: 497 AN: 4816

European-Finnish (FIN) AF: 0.214 AC: 2262 AN: 10570

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.244 AC: 16579 AN: 67984

Other (OTH) AF: 0.190 AC: 401 AN: 2112

Alfa AF: 0.203 Hom.: 1556

Bravo AF: 0.195

Asia WGS AF: 0.0730 AC: 254 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	9.0
DANN	Benign	0.72
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs4553261; hg19: chr10-71375789;