rs10455590

Variant names:

• chr6-65888301-G-A
• rs10455590

Your query was ambiguous. Multiple possible variants found:

• chr6-65888301-G-A
• chr6-65888301-G-C
• chr6-65888301-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.337 in 152,000 control chromosomes in the GnomAD database, including 9,956 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 0.34 (9956 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.190

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.447 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: 0.338 AC: 51285 AN: 151880 Hom.: 9957 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.337 AC: 51290 AN: 152000 Hom.: 9956 Cov.: 32 AF XY: 0.332 AC XY: 24626 AN XY: 74272

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.484

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.296

Gnomad4 FIN AF: 0.409

Gnomad4 NFE AF: 0.451

Gnomad4 OTH AF: 0.369

Alfa AF: 0.437 Hom.: 15383

Bravo AF: 0.322

Asia WGS AF: 0.224 AC: 782 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.6
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10455590; hg19: chr6-66598194;