chr1-17305969-C-G

Position:

• chr1-17305969-C-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 0.108 in 152,206 control chromosomes in the GnomAD database, including 1,196 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 0.11 (1196 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.691

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 (NFE) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.17305969C>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16401 AN: 152086 Hom.: 1195 Cov.: 32

Gnomad AFR AF: 0.0340

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.0895

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0521

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.108 AC: 16403 AN: 152206 Hom.: 1196 Cov.: 32 AF XY: 0.107 AC XY: 7997 AN XY: 74406

Gnomad4 AFR AF: 0.0340

Gnomad4 AMR AF: 0.0893

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0523

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.105

Bravo AF: 0.0974

Asia WGS AF: 0.0290 AC: 102 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	1.3
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs34324150; hg19: chr1-17632464; COSMIC: COSV64925257;