17-78930194-G-T

Variant names:

• chr17-78930194-G-T
• rs7501477

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 0.154 in 151,790 control chromosomes in the GnomAD database, including 2,276 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 0.15 (2276 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.545
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.269 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: 0.154 AC: 23334 AN: 151674 Hom.: 2259 Cov.: 30

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.0363

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.0760

Gnomad FIN AF: 0.0690

Gnomad MID AF: 0.138

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.154 AC: 23387 AN: 151790 Hom.: 2276 Cov.: 30 AF XY: 0.149 AC XY: 11035 AN XY: 74230

African (AFR) AF: 0.273 AC: 11281 AN: 41358

American (AMR) AF: 0.116 AC: 1765 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 363 AN: 3466

East Asian (EAS) AF: 0.110 AC: 561 AN: 5106

South Asian (SAS) AF: 0.0759 AC: 364 AN: 4798

European-Finnish (FIN) AF: 0.0690 AC: 731 AN: 10598

Middle Eastern (MID) AF: 0.152 AC: 44 AN: 290

European-Non Finnish (NFE) AF: 0.117 AC: 7935 AN: 67894

Other (OTH) AF: 0.147 AC: 310 AN: 2106

Alfa AF: 0.0497 Hom.: 55

Bravo AF: 0.165

Asia WGS AF: 0.119 AC: 414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.0
DANN	Benign	0.71
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs7501477; hg19: chr17-76926276;