rs1219515

chr10-121671731-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;