rs983085

Positions:

• chr17-71215920-A-G
• chr17-71215920-A-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 0.515 in 152,020 control chromosomes in the GnomAD database, including 21,581 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 0.51 (21581 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.218

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.715 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: 0.515 AC: 78160 AN: 151902 Hom.: 21550 Cov.: 32

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.515 AC: 78235 AN: 152020 Hom.: 21581 Cov.: 32 AF XY: 0.502 AC XY: 37306 AN XY: 74292

Gnomad4 AFR AF: 0.722

Gnomad4 AMR AF: 0.433

Gnomad4 ASJ AF: 0.320

Gnomad4 EAS AF: 0.361

Gnomad4 SAS AF: 0.275

Gnomad4 FIN AF: 0.348

Gnomad4 NFE AF: 0.475

Gnomad4 OTH AF: 0.470

Alfa AF: 0.454 Hom.: 22014

Bravo AF: 0.534

Asia WGS AF: 0.346 AC: 1207 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.4
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs983085; hg19: chr17-69212061;