rs1219515

Variant names:

• chr10-121671731-G-A
• rs1219515

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 0.0673 in 152,234 control chromosomes in the GnomAD database, including 393 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 0.067 (393 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.47

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0832 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: 0.0673 AC: 10235 AN: 152116 Hom.: 394 Cov.: 33

Gnomad AFR AF: 0.0534

Gnomad AMI AF: 0.0681

Gnomad AMR AF: 0.0672

Gnomad ASJ AF: 0.0667

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0255

Gnomad FIN AF: 0.0583

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0850

Gnomad OTH AF: 0.0699

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

GnomAD4 genome AF: 0.0673 AC: 10241 AN: 152234 Hom.: 393 Cov.: 33 AF XY: 0.0650 AC XY: 4836 AN XY: 74450

Gnomad4 AFR AF: 0.0535

Gnomad4 AMR AF: 0.0669

Gnomad4 ASJ AF: 0.0667

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0257

Gnomad4 FIN AF: 0.0583

Gnomad4 NFE AF: 0.0850

Gnomad4 OTH AF: 0.0691

Alfa AF: 0.0726 Hom.: 51

Bravo AF: 0.0668

Asia WGS AF: 0.0150 AC: 52 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.0040
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1219515; hg19: chr10-123431245;