17-56701456-A-T

Variant names:

• chr17-56701456-A-T
• rs227724

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 0.306 in 152,068 control chromosomes in the GnomAD database, including 7,416 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 0.31 (7416 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 40 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.334 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: 0.307 AC: 46575 AN: 151950 Hom.: 7416 Cov.: 31

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.306 AC: 46590 AN: 152068 Hom.: 7416 Cov.: 31 AF XY: 0.310 AC XY: 23031 AN XY: 74322

African (AFR) AF: 0.244 AC: 10137 AN: 41494

American (AMR) AF: 0.251 AC: 3841 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 913 AN: 3468

East Asian (EAS) AF: 0.281 AC: 1451 AN: 5160

South Asian (SAS) AF: 0.304 AC: 1467 AN: 4826

European-Finnish (FIN) AF: 0.442 AC: 4668 AN: 10568

Middle Eastern (MID) AF: 0.223 AC: 65 AN: 292

European-Non Finnish (NFE) AF: 0.337 AC: 22924 AN: 67958

Other (OTH) AF: 0.277 AC: 584 AN: 2110

Alfa AF: 0.322 Hom.: 4484

Bravo AF: 0.288

Asia WGS AF: 0.312 AC: 1083 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	0.45
DANN	Benign	0.85
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs227724; hg19: chr17-54778817;