rs17655652

Positions:

• chr7-44541392-T-C

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 0.268 in 759,692 control chromosomes in the GnomAD database, including 31,190 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 0.22 (4712 hom., cov: 33)
  • Exomes 𝑓: 0.28 (26478 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.434

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33315 AN: 152094 Hom.: 4712 Cov.: 33

Gnomad AFR AF: 0.0644

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.00964

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.259

GnomAD4 exome AF: 0.280 AC: 170341 AN: 607480 Hom.: 26478 AF XY: 0.280 AC XY: 87414 AN XY: 312004

Gnomad4 AFR exome AF: 0.0593

Gnomad4 AMR exome AF: 0.230

Gnomad4 ASJ exome AF: 0.279

Gnomad4 EAS exome AF: 0.0121

Gnomad4 SAS exome AF: 0.249

Gnomad4 FIN exome AF: 0.235

Gnomad4 NFE exome AF: 0.321

Gnomad4 OTH exome AF: 0.263

GnomAD4 genome AF: 0.219 AC: 33313 AN: 152212 Hom.: 4712 Cov.: 33 AF XY: 0.213 AC XY: 15870 AN XY: 74406

Gnomad4 AFR AF: 0.0643

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.270

Gnomad4 EAS AF: 0.00947

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.226

Gnomad4 NFE AF: 0.316

Gnomad4 OTH AF: 0.256

Alfa AF: 0.294 Hom.: 9463

Bravo AF: 0.213

Asia WGS AF: 0.122 AC: 426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	13
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17655652; hg19: chr7-44580991;