17-63899888-T-C

Variant names:

• chr17-63899888-T-C
• rs2854160

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 0.681 in 151,734 control chromosomes in the GnomAD database, including 36,097 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 0.68 (36097 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.62

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.787 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: 0.681 AC: 103203 AN: 151616 Hom.: 36050 Cov.: 32

Gnomad AFR AF: 0.794

Gnomad AMI AF: 0.793

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.562

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.674

Gnomad OTH AF: 0.689

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

GnomAD4 genome AF: 0.681 AC: 103299 AN: 151734 Hom.: 36097 Cov.: 32 AF XY: 0.670 AC XY: 49632 AN XY: 74132

Gnomad4 AFR AF: 0.794

Gnomad4 AMR AF: 0.608

Gnomad4 ASJ AF: 0.732

Gnomad4 EAS AF: 0.487

Gnomad4 SAS AF: 0.424

Gnomad4 FIN AF: 0.562

Gnomad4 NFE AF: 0.674

Gnomad4 OTH AF: 0.687

Alfa AF: 0.673 Hom.: 37251

Bravo AF: 0.693

Asia WGS AF: 0.479 AC: 1671 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.055
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2854160; hg19: chr17-61977248;