17-78213692-G-C

Variant names:

• chr17-78213692-G-C
• rs8073069

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.325 in 151,394 control chromosomes in the GnomAD database, including 8,444 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 0.32 (8444 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 30 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49140 AN: 151302 Hom.: 8436 Cov.: 31

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.325 AC: 49181 AN: 151394 Hom.: 8444 Cov.: 31 AF XY: 0.324 AC XY: 23937 AN XY: 73894

African (AFR) AF: 0.456 AC: 18802 AN: 41208

American (AMR) AF: 0.313 AC: 4770 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 950 AN: 3466

East Asian (EAS) AF: 0.241 AC: 1239 AN: 5136

South Asian (SAS) AF: 0.321 AC: 1542 AN: 4802

European-Finnish (FIN) AF: 0.281 AC: 2911 AN: 10364

Middle Eastern (MID) AF: 0.292 AC: 84 AN: 288

European-Non Finnish (NFE) AF: 0.267 AC: 18100 AN: 67872

Other (OTH) AF: 0.297 AC: 626 AN: 2110

Alfa AF: 0.307 Hom.: 926

Bravo AF: 0.333

Asia WGS AF: 0.285 AC: 992 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.11
DANN	Benign	0.63
PhyloP100		-1.3
PromoterAI		0.013	Neutral

Splicing

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

Other links and lift over

dbSNP: rs8073069; hg19: chr17-76209773;