17-49486650-T-C

Variant names:

• chr17-49486650-T-C
• rs1035050

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 0.351 in 152,072 control chromosomes in the GnomAD database, including 11,140 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 0.35 (11140 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.544

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.745 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: 0.352 AC: 53415 AN: 151954 Hom.: 11145 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.324

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.765

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.351 AC: 53426 AN: 152072 Hom.: 11140 Cov.: 32 AF XY: 0.353 AC XY: 26216 AN XY: 74348

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.446

Gnomad4 ASJ AF: 0.376

Gnomad4 EAS AF: 0.765

Gnomad4 SAS AF: 0.452

Gnomad4 FIN AF: 0.375

Gnomad4 NFE AF: 0.416

Gnomad4 OTH AF: 0.397

Alfa AF: 0.417 Hom.: 30950

Bravo AF: 0.348

Asia WGS AF: 0.539 AC: 1876 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1035050; hg19: chr17-47564012;