17-39895095-A-G

Variant names:

• chr17-39895095-A-G
• rs8067378

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 0.496 in 152,022 control chromosomes in the GnomAD database, including 18,923 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 0.50 (18923 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 155 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 = 0.529 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: 0.496 AC: 75353 AN: 151904 Hom.: 18879 Cov.: 32

Gnomad AFR AF: 0.534

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.496 AC: 75460 AN: 152022 Hom.: 18923 Cov.: 32 AF XY: 0.495 AC XY: 36810 AN XY: 74296

African (AFR) AF: 0.535 AC: 22154 AN: 41442

American (AMR) AF: 0.445 AC: 6791 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1614 AN: 3468

East Asian (EAS) AF: 0.270 AC: 1398 AN: 5176

South Asian (SAS) AF: 0.398 AC: 1920 AN: 4824

European-Finnish (FIN) AF: 0.574 AC: 6060 AN: 10566

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.497 AC: 33783 AN: 67974

Other (OTH) AF: 0.475 AC: 999 AN: 2102

Alfa AF: 0.492 Hom.: 80769

Bravo AF: 0.482

Asia WGS AF: 0.417 AC: 1450 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	0.27
DANN	Benign	0.43
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs8067378; hg19: chr17-38051348;