rs220457

Variant names:

• chr17-31775616-C-T
• rs220457

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.900 AC: 37383 AN: 41540

American (AMR) AF: 0.821 AC: 12552 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.739 AC: 2564 AN: 3470

East Asian (EAS) AF: 0.820 AC: 4249 AN: 5180

South Asian (SAS) AF: 0.774 AC: 3738 AN: 4828

European-Finnish (FIN) AF: 0.750 AC: 7932 AN: 10574

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.777 AC: 52786 AN: 67974

Other (OTH) AF: 0.819 AC: 1729 AN: 2110

Alfa AF: 0.786 Hom.: 159857

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
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs220457; hg19: chr17-30102635;