rs220457

chr17-31775616-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 0.814 in 152,170 control chromosomes in the GnomAD database, including 50,708 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 0.81 (50708 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.892 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: 0.814 AC: 123762 AN: 152052 Hom.: 50664 Cov.: 32

Gnomad AFR AF: 0.900

Gnomad AMI AF: 0.792

Gnomad AMR AF: 0.821

Gnomad ASJ AF: 0.739

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.775

Gnomad FIN AF: 0.750

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.777

Gnomad OTH AF: 0.817

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

GnomAD4 genome AF: 0.814 AC: 123867 AN: 152170 Hom.: 50708 Cov.: 32 AF XY: 0.813 AC XY: 60478 AN XY: 74402

Gnomad4 AFR AF: 0.900

Gnomad4 AMR AF: 0.821

Gnomad4 ASJ AF: 0.739

Gnomad4 EAS AF: 0.820

Gnomad4 SAS AF: 0.774

Gnomad4 FIN AF: 0.750

Gnomad4 NFE AF: 0.777

Gnomad4 OTH AF: 0.819

Alfa AF: 0.781 Hom.: 82132

Bravo AF: 0.821

Asia WGS AF: 0.848 AC: 2948 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	1.0
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs220457; hg19: chr17-30102635;