rs17161983

chr7-99866195-A-G

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 0.0367 in 345,052 control chromosomes in the GnomAD database, including 1,236 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 0.066 (1029 hom., cov: 32)
  • Exomes 𝑓: 0.014 (207 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.16

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.217 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: 0.0659 AC: 10024 AN: 152100 Hom.: 1028 Cov.: 32

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0343

Gnomad ASJ AF: 0.00462

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.00745

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.00234

Gnomad OTH AF: 0.0580

GnomAD4 exome AF: 0.0136 AC: 2617 AN: 192834 Hom.: 207 AF XY: 0.0124 AC XY: 1232 AN XY: 98974

Gnomad4 AFR exome AF: 0.241

Gnomad4 AMR exome AF: 0.0524

Gnomad4 ASJ exome AF: 0.00402

Gnomad4 EAS exome AF: 0.000352

Gnomad4 SAS exome AF: 0.00998

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00272

Gnomad4 OTH exome AF: 0.0299

GnomAD4 genome AF: 0.0660 AC: 10051 AN: 152218 Hom.: 1029 Cov.: 32 AF XY: 0.0638 AC XY: 4749 AN XY: 74446

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.0343

Gnomad4 ASJ AF: 0.00462

Gnomad4 EAS AF: 0.000770

Gnomad4 SAS AF: 0.00745

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00234

Gnomad4 OTH AF: 0.0588

Alfa AF: 0.0130 Hom.: 229

Bravo AF: 0.0775

Asia WGS AF: 0.0270 AC: 94 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.044
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17161983; hg19: chr7-99463818;