rs1576313

Positions:

• chr10-18846766-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 0.186 in 151,954 control chromosomes in the GnomAD database, including 2,920 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 0.19 (2920 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0490

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 (AFR) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28303 AN: 151836 Hom.: 2920 Cov.: 33

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.0951

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.186 AC: 28318 AN: 151954 Hom.: 2920 Cov.: 33 AF XY: 0.183 AC XY: 13582 AN XY: 74270

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.121

Gnomad4 EAS AF: 0.232

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.0951

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.190

Alfa AF: 0.157 Hom.: 913

Bravo AF: 0.208

Asia WGS AF: 0.195 AC: 674 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.4
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1576313; hg19: chr10-19135695;