chr17-69958971-T-C

Position:

• chr17-69958971-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 0.733 in 152,116 control chromosomes in the GnomAD database, including 41,154 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 0.73 (41154 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.362

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.69958971T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.732 AC: 111317 AN: 151998 Hom.: 41104 Cov.: 32

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.734

Gnomad ASJ AF: 0.704

Gnomad EAS AF: 0.960

Gnomad SAS AF: 0.850

Gnomad FIN AF: 0.698

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.733 AC: 111427 AN: 152116 Hom.: 41154 Cov.: 32 AF XY: 0.736 AC XY: 54742 AN XY: 74358

Gnomad4 AFR AF: 0.790

Gnomad4 AMR AF: 0.734

Gnomad4 ASJ AF: 0.704

Gnomad4 EAS AF: 0.960

Gnomad4 SAS AF: 0.850

Gnomad4 FIN AF: 0.698

Gnomad4 NFE AF: 0.678

Gnomad4 OTH AF: 0.716

Alfa AF: 0.698 Hom.: 4621

Bravo AF: 0.739

Asia WGS AF: 0.895 AC: 3112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.82
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs180075; hg19: chr17-67955112;