rs10455025

Variant names:

• chr5-111069301-A-C
• rs10455025

Your query was ambiguous. Multiple possible variants found:

• chr5-111069301-A-C
• chr5-111069301-A-G
• chr5-111069301-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 0.242 in 152,146 control chromosomes in the GnomAD database, including 5,707 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 0.24 (5707 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.484
• Publications: 25 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.34 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: 0.242 AC: 36740 AN: 152028 Hom.: 5706 Cov.: 32

Gnomad AFR AF: 0.0750

Gnomad AMI AF: 0.452

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.0408

Gnomad SAS AF: 0.0898

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.242 AC: 36747 AN: 152146 Hom.: 5707 Cov.: 32 AF XY: 0.234 AC XY: 17442 AN XY: 74388

African (AFR) AF: 0.0748 AC: 3109 AN: 41558

American (AMR) AF: 0.278 AC: 4247 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.369 AC: 1281 AN: 3468

East Asian (EAS) AF: 0.0407 AC: 211 AN: 5180

South Asian (SAS) AF: 0.0911 AC: 439 AN: 4818

European-Finnish (FIN) AF: 0.289 AC: 3060 AN: 10578

Middle Eastern (MID) AF: 0.247 AC: 72 AN: 292

European-Non Finnish (NFE) AF: 0.344 AC: 23342 AN: 67948

Other (OTH) AF: 0.272 AC: 574 AN: 2110

Alfa AF: 0.311 Hom.: 10079

Bravo AF: 0.241

Asia WGS AF: 0.101 AC: 351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.52
DANN	Benign	0.56
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs10455025; hg19: chr5-110404999;