rs17774576

chr10-49292414-C-Gchr10-49292414-C-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 0.0849 in 152,252 control chromosomes in the GnomAD database, including 791 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 0.085 (791 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.531

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.121 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: 0.0850 AC: 12932 AN: 152134 Hom.: 790 Cov.: 32

Gnomad AFR AF: 0.0220

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.0921

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0240

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.0849 AC: 12929 AN: 152252 Hom.: 791 Cov.: 32 AF XY: 0.0837 AC XY: 6233 AN XY: 74442

Gnomad4 AFR AF: 0.0219

Gnomad4 AMR AF: 0.0919

Gnomad4 ASJ AF: 0.128

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0239

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.123

Gnomad4 OTH AF: 0.100

Alfa AF: 0.0552 Hom.: 74

Bravo AF: 0.0828

Asia WGS AF: 0.0150 AC: 53 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	5.9
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17774576; hg19: chr10-50500459;