rs575338

Variant names:

• chr10-100367735-A-G
• rs575338

Your query was ambiguous. Multiple possible variants found:

• chr10-100367735-A-G
• chr10-100367735-A-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 0.892 in 152,234 control chromosomes in the GnomAD database, including 60,819 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 0.89 (60819 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.237

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.892 AC: 135710 AN: 152116 Hom.: 60760 Cov.: 33

Gnomad AFR AF: 0.942

Gnomad AMI AF: 0.905

Gnomad AMR AF: 0.882

Gnomad ASJ AF: 0.837

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.968

Gnomad FIN AF: 0.869

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.857

Gnomad OTH AF: 0.877

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

GnomAD4 genome AF: 0.892 AC: 135829 AN: 152234 Hom.: 60819 Cov.: 33 AF XY: 0.895 AC XY: 66633 AN XY: 74426

Gnomad4 AFR AF: 0.942

Gnomad4 AMR AF: 0.882

Gnomad4 ASJ AF: 0.837

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.968

Gnomad4 FIN AF: 0.869

Gnomad4 NFE AF: 0.857

Gnomad4 OTH AF: 0.879

Alfa AF: 0.867 Hom.: 16378

Bravo AF: 0.893

Asia WGS AF: 0.973 AC: 3378 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.80
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs575338; hg19: chr10-102127492;