17-7071647-A-G

Position:

• chr17-7071647-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 0.955 in 152,172 control chromosomes in the GnomAD database, including 69,534 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 0.95 (69534 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.984 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.7071647A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.955 AC: 145138 AN: 152054 Hom.: 69480 Cov.: 30

Gnomad AFR AF: 0.901

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.949

Gnomad ASJ AF: 0.986

Gnomad EAS AF: 0.795

Gnomad SAS AF: 0.974

Gnomad FIN AF: 0.990

Gnomad MID AF: 0.997

Gnomad NFE AF: 0.991

Gnomad OTH AF: 0.956

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

GnomAD4 genome AF: 0.955 AC: 145252 AN: 152172 Hom.: 69534 Cov.: 30 AF XY: 0.954 AC XY: 70987 AN XY: 74392

Gnomad4 AFR AF: 0.902

Gnomad4 AMR AF: 0.949

Gnomad4 ASJ AF: 0.986

Gnomad4 EAS AF: 0.795

Gnomad4 SAS AF: 0.975

Gnomad4 FIN AF: 0.990

Gnomad4 NFE AF: 0.991

Gnomad4 OTH AF: 0.955

Alfa AF: 0.967 Hom.: 12801

Bravo AF: 0.948

Asia WGS AF: 0.896 AC: 3117 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	6.7
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7218942; hg19: chr17-6974966;